NPC1L1 orthologues

ABSTRACT

The present invention provides, in part, NPC1L1 from various species. Methods of using the NPC1L1 polypeptides and polynucleotide set forth herein, e.g., in screening assays, are also set forth.

This application claims the benefit of U.S. provisional patent application No. 60/776,394, filed Feb. 24, 2006, which is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to polynucleotides and polypeptides encoding NPC1L1 from various species and uses thereof.

BACKGROUND OF THE INVENTION

A factor leading to development of vascular disease, a leading cause of death in industrialized nations, is elevated serum cholesterol. It is estimated that 19% of Americans between the ages of 20 and 74 years of age have high serum cholesterol. The most prevalent form of vascular disease is arteriosclerosis, a condition associated with the thickening and hardening of the arterial wall. Arteriosclerosis of the large vessels is referred to as atherosclerosis. Atherosclerosis is the predominant underlying factor in vascular disorders such as coronary artery disease, aortic aneurysm, arterial disease of the lower extremities and cerebrovascular disease.

Cholesteryl esters are a major component of atherosclerotic lesions and the major storage form of cholesterol in arterial wall cells. Formation of cholesteryl esters is also a step in the intestinal absorption of dietary cholesterol. Thus, inhibition of cholesteryl ester formation and reduction of serum cholesterol can inhibit the progression of atherosclerotic lesion formation, decrease the accumulation of cholesteryl esters in the arterial wall, and block the intestinal absorption of dietary cholesterol.

The regulation of whole-body cholesterol homeostasis in mammals and animals involves the regulation of intestinal cholesterol absorption, cellular cholesterol trafficking, dietary cholesterol and modulation of cholesterol biosynthesis, bile acid biosynthesis, steroid biosynthesis and the catabolism of the cholesterol-containing plasma lipoproteins. Regulation of intestinal cholesterol absorption has proven to be an effective means by which to regulate serum cholesterol levels. For example, a cholesterol absorption inhibitor, ezetimibe (

has been shown to be effective in this regard. A pharmaceutical composition containing ezetimibe is commercially available from Merck/Schering-Plough Pharmaceuticals, Inc. under the tradename Zetia®. Identification of a gene target through which ezetimibe acts is important to understanding the process of cholesterol absorption and to the development of other, novel absorption inhibitors.

The molecular target through which ezetimibe acts, in humans, rats and mice, has been identified previously to be NPC1L1 (also known as NPC3; published U.S. patent application no. 2004/0161838; Genbank Accession No. AF192522; Davies, et al., (2000) Genomics 65(2):137-45 and Ioannou, (2000) Mol. Genet. Metab. 71(1-2):175-81).

There remains a need in the art for the identification of orthologues of NPC1L1, for example, from non-human animals such as canines, rabbits, hamsters, and monkeys. Identification of such targets would aid in the discovery and development of both human and non-human, veterinary treatments for hyperlipidemia, hypertriglyceridemia and/or hypercholesterolemia which target NPC1L1.

SUMMARY OF THE INVENTION

The present invention addressed the need in the art for veterinary and human treatments for cardiovascular disorders therein (e.g., hyperlipidemia, hypertriglyceridemia, or hypercholesterolemia), in part, by providing orthologues of NPC1L1 from rabbit, hamster, canine and monkey species.

The present invention provides, an isolated polypeptide (e.g., an antigenic polypeptide) comprising an amino acid selected from the group consisting of: 527 or more contiguous amino acids from SEQ ID NO: 2; 42 or more contiguous amino acids from SEQ ID NO: 4; 70 or more contiguous amino acids from SEQ ID NO: 6; 84 or more contiguous amino acids from SEQ ID NO: 8; and 104 or more contiguous amino acids from SEQ ID NO: 10. In an embodiment of the invention, the isolated polypeptide comprises an amino acid sequence selected from SEQ ID NOs: 2, 4, 6, 8 and 10. In an embodiment of the invention, the polypeptide is labeled with a member selected from the group consisting of ³²P, ³⁵S, ³H, ^(99m)Tc, ¹²³I, ¹¹¹In, ⁶⁸Ga, ¹⁸F, ¹²⁵I, ¹³¹I, ^(113m)In, ⁷⁶Br, ⁶⁷Ga, ^(99m)Tc, ¹²³I, ¹¹¹In and ⁶⁸Ga. The present invention also provides an isolated fusion polypeptide comprising the polypeptide of claim 1 fused to a heterologous polypeptide (e.g., glutathione-S-transferase (GST), a hexahistidine (His6) tag, a maltose binding protein (MBP) tag, a haemagglutinin (HA) tag, a cellulose binding protein (CBP) tag and a myc tag). An embodiment of the invention also includes a polypeptide of the invention, complexed with a member selected from the group consisting of compounds 1-9, a sterol (e.g., cholesterol), and a 5α-stanol; or a detectably labeled (e.g., ³H or ¹²⁵I) version thereof.

The present invention further provides an isolated polynucleotide which hybridizes to a polynucleotide encoding a polypeptide of the invention (e.g., as set forth above) under high stringency hybridization conditions. An embodiment of the invention includes an isolated polynucleotide encoding a polypeptide of the invention. An embodiment of the invention includes an isolated polynucleotide comprising a nucleotide sequence selected from SEQ ID NOs: 1, 3, 5, 7 and 9. The present invention also includes a recombinant vector comprising a polynucleotide of the invention (e.g., as set forth above). The present invention also includes an isolated host cell comprising a vector of the invention.

The present invention further provides an isolated antibody (e.g., monoclonal, polyclonal, a human antibody, a canine antibody, a hamster antibody, a rabbit antibody, a rhesus monkey antibody, a cynomolgus monkey antibody, chimeric, anti-idiotypic, recombinant and/or a humanized antibody) which specifically binds to a polypeptide (e.g., an antigenic polypeptide) of the invention. The present invention also includes a complex comprising an antibody of the invention bound to a polypeptide of the invention (e.g., a complex between an isolated antibody and a polypeptide in the body of a patient, e.g., in the intestinal tract of the patient or an in vitro complex). The present invention further provides a pharmaceutical formulation comprising an antibody of the invention along with a pharmaceutically acceptable carrier.

The present invention further provides an isolated canine, hamster, rabbit, rhesus monkey or cynomolgus monkey cell (e.g., an enterocyte) which lacks a gene which encodes a functional canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 protein (e.g., SEQ ID NO: 2, 4, 6, 8 or 10), respectively. In an embodiment of the invention, the cell is isolated from duodenum, gall bladder, liver, small intestine or stomach tissue.

The present also provides a kit comprising: a substituted azetidinone (e.g., ezetimibe) in a pharmaceutical dosage form; and information indicating that canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 is a target of the substituted azetidinone. In an embodiment of the invention, the dosage form is a tablet comprising 10 mg ezetimibe. In an embodiment of the invention, the kit further comprises simvastatin in a pharmaceutical dosage form (e.g., wherein the pharmaceutical dosage form comprises 5 mg, 10 mg, 20 mg, 40 mg or 80 mg simvastatin). In an embodiment of the invention, the simvastatin in pharmaceutical dosage form and the ezetimibe in pharmaceutical dosage form are associated in a single pill or tablet.

The present invention also provides a mutant transgenic dog, hamster, rabbit, rhesus monkey or cynomolgus monkey comprising a homozygous mutation of endogenous, chromosomal NPC1L1 wherein said dog, hamster, rabbit, rhesus monkey or cynomolgus monkey does not produce any functional NPC1L1 protein. In an embodiment of the invention, the animal exhibits a reduced serum sterol or 5α-stanol level, a reduced liver sterol or 5α-stanol level or a reduced level of intestinal absorption of sterol or 5α-stanol. An offspring or progeny of the dog, hamster, rabbit, rhesus monkey or cynomolgus monkey which has inherited a mutated NPC1L1 allele of said dog, hamster, rabbit, rhesus monkey or cynomolgus monkey is also within the scope of the present invention.

The present invention also includes a method for making a polypeptide comprising culturing a host cell (e.g., bacterial cell, an insect cell or a mammalian cell) of the invention (e.g., comprising a vector comprising a polynucleotide that encodes a polypeptide of the invention) under conditions in which the polynucleotide is expressed. In an embodiment of the invention, the polypeptide is isolated from the culture. The present invention further provides any polypeptide produced by said method.

The present invention further provides a method for identifying (i) an antagonist of NPC1L1 (e.g., human NPC1L1) or (ii) a substance useful for the treatment or prevention of hyperlipidemia, hypertriglyceridemia, hycholesterolemia, atherosclerosis or arteriosclerosis or (iii) an inhibitor of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption comprising: (a) contacting a host cell (e.g., chinese hamster ovary (CHO) cell, a J774 cell, a macrophage cell or a Caco2 cell) expressing an NPC1L1 polypeptide of the invention e.g., polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 2, 4, 6, 8 and 10 or a functional fragment thereof on a cell surface, in the presence of a known amount of detectably labeled substance which is known to bind to said polypeptide (e.g., a radiolabeled (e.g., ³H or ¹²⁵I) compound represented by structural formula 1, 2, 3, 4, 5, 6, 7, 8 or 9) with a sample to be tested for the presence of the antagonist; and (b) measuring the amount of the detectably labeled substance specifically bound to the polypeptide; wherein an NPC1L1 antagonist in the sample is identified by measuring substantially reduced binding of the detectably labeled substance to the polypeptide, compared to what would be measured in the absence of such an antagonist. The present invention also provides a method for inhibiting NPC1L1 mediated sterol or 5α-stanol uptake, in a subject, by administering, to the subject, a substance identified by such a method.

The present invention further provides a method for identifying (i) an antagonist of NPC1L1 (e.g., human NPC1L1) or (ii) a substance useful for the treatment or prevention of hyperlipidemia, hypertriglyceridemia, hycholesterolemia, atherosclerosis or arteriosclerosis or (iii) an inhibitor of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption comprising: (a) placing, in an aqueous suspension, a plurality of support particles, impregnated with a fluorescer (e.g., yttrium silicate, yttrium oxide, diphenyloxazole or polyvinyltoluene), to which a host cell (e.g., chinese hamster ovary (CHO) cell, a J774 cell, a macrophage cell or a Caco2 cell) expressing a polypeptide of the invention (e.g., comprising an amino acid sequence selected from SEQ ID NOs: 2, 4, 6, 8 and 10 or a functional fragment thereof) on a cell surface is attached; (b) adding, to the suspension, a radiolabeled substance which is known to bind said polypeptide (e.g., a radiolabeled (e.g., ³H or ¹²⁵I) compound represented by structural formula 1, 2, 3, 4, 5, 6, 7, 8 or 9) and a sample to be tested for the presence of the antagonist, wherein the radiolabel emits radiation energy capable of activating the fluorescer upon binding of the substance to the polypeptide to produce light energy, whereas radiolabeled substance that does not bind to the polypeptide is, generally, too far removed from the support particles to enable the radioactive energy to activate the fluorescer; and (c) measuring the light energy emitted by the fluorescer in the suspension; wherein an NPC1L1 antagonist in the sample is identified by measuring substantially reduced light energy emission, compared to what would be measured in the absence of such an antagonist. The present invention also provides a method for inhibiting NPC1L1 mediated sterol or 5α-stanol uptake, in a subject, by administering, to the subject, a substance identified by such a method.

The present invention also provides a method for identifying (i) an antagonist of NPC1L1 (e.g., human NPC1L1) or (ii) a substance useful for the treatment or prevention of hyperlipidemia, hypertriglyceridemia, hycholesterolemia, atherosclerosis or arteriosclerosis or (iii) an inhibitor of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption comprising: (a) contacting a host cell (e.g., chinese hamster ovary (CHO) cell, a J774 cell, a macrophage cell or a Caco2 cell) expressing an NPC1L1 polypeptide of the invention (e.g., comprising an amino acid sequence selected from SEQ ID NOs: 2, 4, 6, 8 and 10 or a functional fragment thereof) on a cell surface with a detectably labeled (e.g., ³H, ¹⁴C and ¹²⁵I) sterol (e.g., cholesterol) or 5α-stanol and with a sample to be tested for the presence of the antagonist; and (b) measuring the amount of detectably labeled sterol or 5α-stanol in the cell; wherein an NPC1L1 antagonist in the sample is identified by measuring substantially reduced detectably labeled sterol or 5α-stanol within the host cell, compared to what would be measured in the absence of such an antagonist. The present invention also provides a method for inhibiting NPC1L1 mediated sterol or 5α-stanol uptake, in a subject, by administering, to the subject, a substance identified by such a method.

The present invention further provides a method for screening a sample for (i) an antagonist of NPC1L1 (e.g., human NPC1L1) or (ii) a substance useful for the treatment or prevention of hyperlipidemia, hypertriglyceridemia, hycholesterolemia, atherosclerosis or arteriosclerosis or (iii) an inhibitor of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption comprising: (a) feeding a sterol or 5α-stanol-containing substance to a first and second animal which is a canine, hamster, rabbit, rhesus monkey or cynomolgus monkey comprising a functional NPC1L1 gene and to a third, mutant animal which is a canine, hamster, rabbit, rhesus monkey or cynomolgus monkey which does not comprise a functional NPC1L1 gene; (b) administering the sample to be tested for the presence of the antagonist to the first animal but not the second animal; (c) measuring the amount of sterol or 5α-stanol absorption in the intestine of said first, second and third animals; and (d) comparing the levels of intestinal sterol or 5α-stanol absorption in said first, second and third animals; wherein the sample is determined to contain the intestinal sterol or 5α-stanol absorption antagonist when the level of intestinal sterol or 5α-stanol absorption in the first animal and third animal are less than the amount of intestinal sterol or 5α-stanol absorption in the second animal. In an embodiment of the invention, the level of sterol or 5α-stanol cholesterol absorption is determined by measuring the level of serum sterol or 5α-stanol in the canine, hamster, rabbit, rhesus monkey or cynomolgus monkey. The present invention also provides a method for inhibiting NPC1L1 mediated sterol or 5α-stanol uptake, in a subject, by administering, to the subject, a substance identified by such a method.

The present invention also provides a method for decreasing the level of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption in a non-human mammalian subject (e.g., a canine such as a dog, hamster, rabbit, rhesus monkey or cynomolgus monkey) comprising reducing the level of expression of endogenous NPC1L1 in the subject. In an embodiment of the invention, the level of expression of NPC1L1 in the subject is reduced by mutating NPC1L1 in the subject.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Ball model of predicted membrane topology of human NPC1L1 (SEQ ID NO: 25). Residues highlighted (black) identify the predicted sterol sensing domain (Carstea et al., Science; 277:228-231 (1997)). Shaded residues (gray) identify amino acids that are not conserved between human and monkey proteins.

FIG. 2. Progressive multiple amino acid sequence alignment using the Clustal W method (Thompson et al., Nucleic Acid Research 22; 4673-80 (1994)). (A) NPC1L1 amino acid sequence pair distances between species comparing percent identity and percent divergence. (B) Phylogenetic tree representation of amino acid sequence alignment using Treeview (Page, 1996).

FIG. 3. Characterization of NPC1L1 binding in multiple species. HEK 293 cells expressing human (A), monkey (B), rat (C), hamster (D), rabbit (E), or canine (F) NPC1L1 were exposed to the indicated concentration of compound 1 for 4 h. The amount of fluorescence bound to the cells was quantified as total binding (open circles). Addition of 100 uM compound 4 was used to determine nonspecific binding (open triangles). Specific binding (filled circles) was determined by subtraction of nonspecific from total binding. The Kd values were calculated using Prism software and are the mean of at least three separate experiments. Competition binding of compound 3 and compound 4 to NPC1L1 is also shown. Binding of compound 1 to HEK 293 cells expressing each species NPC1L1 in the presence of the indicated concentration of compound 3 (open circles) or compound 4 (filled circles) was determined. Ki values were calculated using Prism software and are the mean of at least three separate experiments.

FIG. 4. Comparison of binding characteristics of compound 1 and compound 2. (A) Structure of compound 1 and compound 2. Saturation binding of [³H]-labeled compound 4 to membranes derived from HEK 293 cells expressing human NPC1L1 (B) or mouse NPC1L1 (C). [³H]compound 4 bound was determined in the absence (total, filled circles) or presence (nonspecific, open circles) of 100 μM unlabeled compound 4. Specific binding (filled triangles) was determined by subtracting nonspecific from total binding. Kd values were determined using Prism software. The Ki of compound 1 and compound 2 at human NPC1L1 (D) and monkey NPC1L1 (E) was determined by competition binding studies using [³H]-labeled compound 4. Studies were performed on membranes from HEK 293 cells expressing human or monkey NPC1L1. Ki values are the mean from at least three separate experiments.

FIG. 5. Correlation of NPC1L1 binding and in vivo efficacy. Data (ED50) from studies assessing in vivo efficacy of compound 3 in human, monkey, hamster, canine, rat, rabbit, and mouse species is plotted as a function of the ability of compound 3 (A) or compound 4 (B) to bind to each species NPC1L1 ortholog.

FIG. 6. Comparison of compound 1 and compound 2 binding to human and monkey NPC1L1. Saturation binding of [³H]-labeled compound 4 to human (A) and monkey (B) NPC1L1 was performed to determine Kd values. The Ki values of compound 1 (triangles) and compound 2 (circles) at human (C) and monkey (D) NPC1L1 were then determined. Ki values were calculated using Prism software and are the mean of three separate experiments.

FIG. 7. Comparison of the amino acid sequences of monkey NPC1L1 (SEQ ID NO: 8), canine NPC1L1 (SEQ ID NO: 2), hamster NPC1L1 (SEQ ID NO: 6), rabbit NPC1L1 (SEQ ID NO: 4), human NPC1L1 (SEQ ID NO: 25), rat NPC1L1 (SEQ ID NO: 28), mouse NPC1L1 (SEQ ID NO: 27) (Altmann et al., Science 303:1201-1204 (2004)), chimpanzee NPC1L1 (SEQ ID NO: 26) (Genbank XM_(—)519072) and cow NPC1L1 (SEQ ID NO: 29) (Genbank XM_(—)588051).

DETAILED DESCRIPTION OF THE INVENTION

The present invention includes any isolated polynucleotide or isolated polypeptide (or any antigenic and/or active fragment thereof) comprising a nucleotide or amino acid sequence referred to, below, in Table 1.

TABLE 1 Polynucleotides and Polypeptides of the Invention. Polynucleotide or Polypeptide Sequence Identifier Canine NPC1L1 polynucleotide SEQ ID NO: 1 Canine NPC1L1 polypeptide SEQ ID NO: 2 Rabbit NPC1L1 polynucleotide SEQ ID NO: 3 Rabbit NPC1L1 polypeptide SEQ ID NO: 4 Hamster NPC1L1 polynucleotide SEQ ID NO: 5 Hamster NPC1L1 polypeptide SEQ ID NO: 6 Rhesus monkey NPC1L1 polynucleotide SEQ ID NO: 7 Rhesus monkey NPC1L1 polypeptide SEQ ID NO: 8 Cynomolgus monkey NPC1L1 SEQ ID NO: 9 polynucleotide Cynomolgus monkey NPC1L1 SEQ ID NO: 10 polypeptide

The term “rhesus monkey” is well known in the art and typically refers to the Rhesus Macaque or the Macaca mulatto.

The term “cynomolgus monkey” is also well known in the art and typically refers to the Macaca fascicularis.

The term “canine” includes any animal of the genus Canis and any species, variety or breed thereof, for example, the domestic dog-Canis familiaris (e.g., beagle). Structural formulas representing compounds 1-9 are as follows:

Molecular Biology

In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (herein “Sambrook, et al., 1989”); DNA Cloning: A Practical Approach, Volumes I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. (1985)); Transcription And Translation (B. D. Hames & S. J. Higgins, eds. (1984)); Animal Cell Culture (R. I. Freshney, ed. (1986)); Immobilized Cells And Enzymes (IRL Press, (1986)); B. Perbal, A Practical Guide To Molecular Cloning (1984); F. M. Ausubel, et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994).

A “polynucleotide”, “nucleic acid” or “nucleic acid molecule” includes the phosphate ester polymeric form of ribonucleosides (adenosine, guanosine, uridine or cytidine; “RNA molecules”) or deoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, or deoxycytidine; “DNA molecules”), or any phosphoester analogs thereof, such as phosphorothioates and thioesters, in single stranded form, double-stranded form or otherwise.

A “polynucleotide sequence”, “nucleic acid sequence” or “nucleotide sequence” is a series of nucleotide bases (also called “nucleotides”) in a nucleic acid, such as DNA or RNA, and means any chain of two or more nucleotides.

A “coding sequence” or a sequence “encoding” an expression product, such as a RNA, polypeptide, protein, or enzyme, is a nucleotide sequence that, when expressed, results in production of the product.

The term “gene” means a DNA sequence that codes for or corresponds to a particular sequence of ribonucleotides or amino acids which comprise all or part of one or more RNA molecules, proteins or enzymes, and may or may not include regulatory DNA sequences, such as promoter sequences, which determine, for example, the conditions under which the gene is expressed. Genes may be transcribed from DNA to RNA which may or may not be translated into an amino acid sequence.

The present invention includes nucleic acid fragments of any of SEQ ID NOs: 1, 3, 5, 7, or 9. For example, the present invention includes any polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, 4, 6, 8, or 10 as well as any polynucleotide encoding a fragment (e.g., an antigenic fragment) of a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, 4, 6, 8, or 10 for example as set forth herein. In an embodiment of the invention, the polynucleotide comprises at least about 1550, 1560, 1570, 1580, 1590, 1600, 1610, 2000, 2500, 3000, 3400, 3800, 3900 or 3950 contiguous nucleotides of SEQ ID NO: 1. In an embodiment of the invention, the polynucleotide comprises at least about 100, 110, 120, 123, 124, 125, 150, 300, 600, 900, 1000, 1500, 2000, 2300, 2600, 2900, 3300, 3500, 3700, 3900 or 3950 contiguous nucleotides of SEQ ID NO: 3. In an embodiment of the invention, the polynucleotide comprises at least about 230, 235, 240, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 300, 500, 700, 900, 1000, 1300, 1500, 1700, 1900, 2000, 2200, 2400, 2600, 2900, 3000, 3300, 3500, 3700, 3800, 3900 or 3950 contiguous nucleotides of SEQ ID NO: 7. In an embodiment of the invention, the polynucleotide comprises at least about 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 500, 700, 900, 1000, 1300, 1500, 1700, 1900, 2000, 2200, 2400, 2600, 2900, 3000, 3300, 3500, 3700, 3800, 3900 or 3950 contiguous nucleotides of SEQ ID NO: 9.

As used herein, the term “oligonucleotide” refers to a nucleic acid, generally of no more than about 100 nucleotides (e.g., 30, 40, 50, 60, 70, 80, or 90), that may be hybridizable to a genomic DNA molecule, a cDNA molecule, or an mRNA molecule encoding a gene, mRNA, cDNA, or other nucleic acid of interest. Oligonucleotides can be labeled, e.g., by incorporation of ³²P-nucleotides, ³H-nucleotides, ¹⁴C-nucleotides, ³⁵S-nucleotides or nucleotides to which a label, such as biotin, has been covalently conjugated. In one embodiment, a labeled oligonucleotide can be used as a probe to detect the presence of a nucleic acid. In another embodiment, oligonucleotides (one or both of which may be labeled) can be used as PCR primers, either for cloning full length or a fragment of the gene, or to detect the presence of nucleic acids. Generally, oligonucleotides are prepared synthetically, preferably on a nucleic acid synthesizer.

A “protein sequence”, “peptide sequence” or “polypeptide sequence” or “amino acid sequence” refers to a series of two or more amino acids in a protein, peptide or polypeptide.

“Protein”, “peptide” or “polypeptide” includes a contiguous string of two or more amino acids. Preferred peptides of the invention include those set forth in any of SEQ ID NOs: 2, 4, 6, 8 or 10 as well as variants and fragments thereof. In an embodiment of the invention, the fragment is an antigenic fragment. In an embodiment, the fragment is an active fragment which is capable of binding to an azetidinone such as ezetimibe or a related compounds such as any of those set forth herein (e.g., any of compounds 1-9)-active fragments are useful, e.g., for identification of NPC1L1 antagonists, for example, in an assay as set forth herein. Such fragments (e.g., antigenic fragments) comprise, in an embodiment of the invention, at least about 10 (e.g., 11, 12, 13, 14, 15, 16, 17, 18 or 19), or at least about 20 (e.g., 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40), or at least about 42 (e.g., 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 110, 120 or 130) or more contiguous amino acid residues from any of SEQ ID NOs: 2, 4, 6, 8, or 10. An embodiment of the invention includes any polypeptide comprising at least about 527 contiguous amino acids from SEQ ID NO: 2 (e.g., 500, 505, 510, 515, 520, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1050, 1100, 1150, 1200, 1250, 1300 or 1320 contiguous amino acids). An embodiment of the invention includes any polypeptide comprising at least about 42 contiguous amino acids from SEQ ID NO: 4 (e.g., 35, 37, 40, 41, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1050, 1100, 1150, 1200, 1250, 1300 or 1320 contiguous amino acids). An embodiment of the invention includes any polypeptide comprising at least about 70 or more contiguous amino acids from SEQ ID NO: 6 (e.g., 60, 65, 67, 69, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1050, 1100, 1150, 1200, 1250, 1300 or 1320 contiguous amino acids). An embodiment of the invention includes any polypeptide comprising at least about 84 or more contiguous amino acids from SEQ ID NO: 8 (e.g., 75, 77, 79, 82, 83, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1320 or 1330 contiguous amino acids). An embodiment of the invention includes any polypeptide comprising at least about 104 or more contiguous amino acids from SEQ ID NO: 10 (e.g., 90, 93, 95, 97, 99, 100, 101, 102, 103, 105, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1320 or 1330 contiguous amino acids. Also included within the scope of the present invention is any polynucleotide that encodes such a polypeptide. In an embodiment of the invention, a polypeptide as set forth above is an antigenic polypeptide.

In an embodiment of the invention, a polypeptide of the invention (e.g., SEQ ID NO: 2, 4, 6, 8 or 10 or any fragment thereof, e.g., as set forth herein) exhibits the ability to bind to ezetimibe or any structurally related compound (e.g., any of compounds 1-9 herein). The scope of the invention also includes any polynucleotide encoding such a polypeptide.

The polypeptides of the invention can be produced by proteolytic cleavage of an intact peptide, by chemical synthesis or by the application of recombinant DNA technology and are not limited to polypeptides delineated by proteolytic cleavage sites. The polypeptides, either alone or cross-linked or conjugated to a carrier molecule to render them more immunogenic, are useful as antigens to elicit the production of antibodies and fragments thereof and are within the scope of the present invention. The antibodies can be used, e.g., in immunoassays for immunoaffinity purification or for inhibition of NPC1L1, etc.

The terms “isolated polynucleotide” or “isolated polypeptide” include a polynucleotide (e.g., RNA or DNA molecule, or a mixed polymer) or a polypeptide, respectively, which are partially (to any degree) or fully separated from other components that are normally found in cells or in recombinant DNA expression systems. These components include, but are not limited to, cell membranes, cell walls, ribosomes, polymerases, serum components and extraneous genomic sequences.

An isolated polynucleotide or polypeptide will, in an embodiment of the invention, be an essentially homogeneous composition.

“Amplification” of DNA as used herein includes the use of polymerase chain reaction (PCR) to increase the concentration of a particular DNA sequence within a mixture of DNA sequences. For a description of PCR see Saiki, et al., Science (1988) 239:487.

A practitioner or ordinary skill in the art could easily isolate and express any of the NPC1L1 genes (e.g., SEQ ID NO: 1, 3, 5, 7 or 9) and proteins (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) set forth herein. For example, a convenient method for obtaining an NPC1L1 gene of the invention is to simply amplify the gene, using standard PCR methods from a cDNA library that was generated from canine, rabbit, hamster, rhesus monkey or cynomolgus monkey tissue or cells. Such a cDNA library can be generated using any of several well known methods in the art. In such a embodiment of the invention, oligonucleotide PCR primers, to be used in PCR amplification of an NPC1L1 of the invention, anneal to the extreme 5′ and 3′ ends of a gene of the invention (e.g., SEQ ID NO: 1, 3, 5, 7, or 9).

The term “host cell” includes any cell of any organism that is selected, modified, transfected, transformed, grown, or used or manipulated in any way, for the production of a substance by the cell, for example the expression or replication, by the cell, of a gene, a DNA or RNA sequence or a protein. Suitable host cells include bacterial cells (e.g., E. coli) and mammalian cells such as chinese hamster ovary (CHO) cells, murine macrophage J774 cells or any other macrophage cell line and human intestinal epithelial Caco2 cells.

The nucleotide sequence of a nucleic acid may be determined by any method known in the art (e.g., chemical sequencing or enzymatic sequencing). “Chemical sequencing” of DNA includes methods such as that of Maxam and Gilbert (1977) (Proc. Natl. Acad. Sci. USA 74:560), in which DNA is randomly cleaved using individual base-specific reactions. “Enzymatic sequencing” of DNA includes methods such as that of Sanger (Sanger, et al., (1977) Proc. Natl. Acad. Sci. USA 74:5463).

The nucleic acids herein may be flanked by natural regulatory (expression control) sequences, or may be associated with heterologous sequences, including promoters, internal ribosome entry sites (IRES) and other ribosome binding site sequences, enhancers, response elements, suppressors, signal sequences, polyadenylation sequences, introns, 5′- and 3′-non-coding regions, and the like.

In general, a “promoter” or “promoter sequence” is a DNA regulatory region capable of binding an RNA polymerase in a cell (e.g., directly or through other promoter-bound proteins or substances) and initiating transcription of a coding sequence. A promoter sequence is, in general, bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at any level. Within the promoter sequence may be found a transcription initiation site (conveniently defined, for example, by mapping with nuclease S1), as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. The promoter may be operably associated with other expression control sequences, including enhancer and repressor sequences or with a nucleic acid of the invention. Promoters which may be used to control gene expression include, but are not limited to, cytomegalovirus (CMV) promoter (U.S. Pat. Nos. 5,385,839 and 5,168,062), the SV40 early promoter region (Benoist, et al., (1981) Nature 290:304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto, et al., (1980) Cell 22:787-797), the herpes thymidine kinase promoter (Wagner, et al., (1981) Proc. Natl. Acad. Sci. USA 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster, et al., (1982) Nature 296:39-42); prokaryotic expression vectors such as the β-lactamase promoter (Villa-Komaroff, et al., (1978) Proc. Natl. Acad. Sci. USA 75:3727-3731), or the tac promoter (DeBoer, et al., (1983) Proc. Natl. Acad. Sci. USA 80:21-25); see also “Useful proteins from recombinant bacteria” in Scientific American (1980) 242:74-94; and promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter or the alkaline phosphatase promoter.

The present invention comprises a nucleotide encoding NPC1L1 or a fragment thereof (e.g., a functional or antigenic fragment) operably associated with a control sequence such as a promoter. A coding sequence is “under the control of”, “functionally associated with” or “operably associated with” transcriptional and translational control sequences in a cell when the sequences direct RNA polymerase mediated transcription of the coding sequence into RNA, preferably mRNA, which then may be RNA spliced (if it contains introns) and, optionally, translated into a protein encoded by the coding sequence.

The terms “express” and “expression” mean allowing or causing the information in a gene, RNA or DNA sequence to become manifest; for example, producing a protein by activating the cellular functions involved in transcription and translation of a corresponding gene. A DNA sequence is expressed in or by a cell to form an “expression product” such as an RNA (e.g., mRNA) or a protein. The expression product itself may also be said to be “expressed” by the cell.

The term “transformation” means the introduction of a nucleic acid into a cell. The introduced gene or sequence may be called a “clone”. A host cell that receives the introduced DNA or RNA has been “transformed” and is a “transformant” or a “clone.” The DNA or RNA introduced to a host cell can come from any source, including cells of the same genus or species as the host cell, or from cells of a different genus or species.

The term “vector” includes a vehicle (e.g., a plasmid) by which a DNA or RNA sequence can be introduced into a host cell, so as to transform the host and, optionally, promote expression and/or replication of the introduced sequence.

The present invention includes any polynucleotide (e.g., comprising a nucleotide sequence of SEQ ID NO: 1, 3, 5, 7 or 9) encoding an NPC1L1 polypeptide (e.g., comprising an amino acid sequence of SEQ ID NO: 2, 4, 6, 8 or 10) in a vector. Vectors that can be used in this invention include plasmids, viruses, bacteriophage, integratable DNA fragments, and other vehicles that may facilitate introduction of the nucleic acids into the genome of the host. Plasmids are the most commonly used form of vector but all other forms of vectors which serve a similar function and which are, or become, known in the art are suitable for use herein. See, e.g., Pouwels, et al., Cloning Vectors: A Laboratory Manual, 1985 and Supplements, Elsevier, N.Y., and Rodriguez et al. (eds.), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, 1988, Buttersworth, Boston, Mass.

The term “expression system” means a host cell and compatible vector which, under suitable conditions, can express a protein or nucleic acid which is carried by the vector and introduced to the host cell. Common expression systems include E. coli host cells and plasmid vectors, insect host cells and Baculovirus vectors, and mammalian host cells and vectors.

Expression of nucleic acids encoding the NPC1L1 polypeptides of this invention can be carried out by conventional methods in either prokaryotic or eukaryotic cells. Although E. coli host cells are employed most frequently in prokaryotic systems, many other bacteria, such as various strains of Pseudomonas and Bacillus, are known in the art and can be used as well. Suitable host cells for expressing nucleic acids encoding the NPC1L1 polypeptides include prokaryotes and higher eukaryotes. Prokaryotes include both gram-negative and gram-positive organisms, e.g., E. coli and B. subtilis. Higher eukaryotes include established tissue culture cell lines from animal cells, both of non-mammalian origin, e.g., insect cells, and birds, and of mammalian origin, e.g., human, primates, and rodents. The present invention comprise any host cell comprising an NPC1L1 polynucleotide of the invention and/or expressing an NPC1L1 polypeptide of the invention, for example, on the cell surface.

Prokaryotic host-vector systems include a wide variety of vectors for many different species. A representative vector for amplifying DNA is pBR322 or many of its derivatives (e.g., pUC18 or 19). Vectors that can be used to express the NPC1L1 polypeptides include, but are not limited to, those containing the lac promoter (pUC-series); trp promoter (pBR322-trp); lpp promoter (the plN-series); lambda-pP or pR promoters (pOTS); or hybrid promoters such as ptac (pDR540). See Brosius et al., “Expression Vectors Employing Lambda-, trp-, lac-, and lpp-derived Promoters”, in Rodriguez and Denhardt (eds.) Vectors: A Survey of Molecular Cloning Vectors and Their Uses, 1988, Buttersworth, Boston, pp. 205-236. Many polypeptides can be expressed, at high levels, in an E. coli/T7 expression system as disclosed in U.S. Pat. Nos. 4,952,496, 5,693,489 and 5,869,320 and in Davanloo, P., et al., (1984) Proc. Natl. Acad. Sci. USA 81: 2035-2039; Studier, F. W., et al., (1986) J. Mol. Biol. 189: 113-130; Roseonberg, A. H., et al., (1987) Gene 56: 125-135; and Dunn, J. J., et al., (1988) Gene 68: 259.

Higher eukaryotic tissue culture cells may also be used for the recombinant production of the NPC1L1 polypeptides of the invention. Although any higher eukaryotic tissue culture cell line might be used, including insect baculovirus expression systems, mammalian cells are preferred. Transformation or transfection and propagation of such cells have become a routine procedure. Examples of useful cell lines include HeLa cells, chinese hamster ovary (CHO) cell lines, J774 cells, Caco2 cells, baby rat kidney (BRK) cell lines, insect cell lines, bird cell lines, and monkey (COS) cell lines. Expression vectors for such cell lines usually include an origin of replication, a promoter, a translation initiation site, RNA splice sites (if genomic DNA is used), a polyadenylation site, and a transcription termination site. These vectors also, usually, contain a selection gene or amplification gene. Suitable expression vectors may be plasmids, viruses, or retroviruses carrying promoters derived, e.g., from such sources as adenovirus, SV40, parvoviruses, vaccinia virus, or cytomegalovirus. Examples of expression vectors include pCR®3.1, pCDNA1, pCD (Okayama, et al., (1985) Mol. Cell Biol. 5:1136), pMC1neo Poly-A (Thomas, et al., (1987) Cell 51:503), pREP8, pSVSPORT and derivatives thereof, and baculovirus vectors such as pAC373 or pAC610. One embodiment of the invention includes membrane bound NPC1L1. In this embodiment, NPC1L1 can be expressed in the cell membrane of a eukaryotic cell and the membrane bound protein can be isolated from the cell by conventional methods which are known in the art.

The present invention also includes fusions which include the NPC1L1 polypeptides and NPC1L1 polynucleotides of the present invention and a second, heterologous polypeptide or polynucleotide moiety (different from the NPC1L1 moiety in the fusion), which may be referred to as a “tag”. The fusions of the present invention include any of the polynucleotides or polypeptides set forth in Table 1 or any subsequence or fragment thereof (discussed above). The fused polypeptides of the invention may be conveniently constructed, for example, by insertion of a polynucleotide of the invention or fragment thereof into an expression vector. The fusions of the invention include tags which facilitate purification or detection. Such tags include green fluorescent protein (GFP) or any mutant thereof (e.g., S65T mutant; see Heim et al., Nature 373: 663-664 (1995)), glutathione-S-transferase (GST), hexahistidine (His6) tags, maltose binding protein (MBP) tags, haemagglutinin (HA) tags, cellulose binding protein (CBP) tags and myc tags. Detectable tags such as ³²P, ³⁵S, ³H, ^(99m)Tc, ¹²³I, ¹¹¹In, ⁶⁸Ga, ¹⁸F, ¹²⁵I, ¹³¹I, ^(113m)In, ⁷⁶Br, ⁶⁷Ga, ^(99m)Tc, ¹²³I, ¹¹¹In and ⁶⁸Ga may also be used to label the polypeptides and polynucleotides of the invention. Methods for constructing and using such fusions are very conventional and well known in the art.

Modifications (e.g., post-translational modifications) that occur in a polypeptide often will be a function of how it is made. For polypeptides made by expressing a cloned gene in a host, for instance, the nature and extent of the modifications, in large part, will be determined by the host cell's post-translational modification capacity and the modification signals present in the polypeptide amino acid sequence. For instance, as is well known, glycosylation often does not occur in bacterial hosts such as E. coli. Accordingly, when glycosylation is desired, a polypeptide can be expressed in a glycosylating host, generally a eukaryotic cell. Insect cells often carry out post-translational glycosylations which are similar to those of mammalian cells. For this reason, insect cell expression systems have been developed to express, efficiently, mammalian proteins having native patterns of glycosylation. An insect cell which may be used in this invention is any cell derived from an organism of the class Insecta. In an embodiment of the invention, the insect is Spodoptera fruigiperda (Sf9 or Sf21) or Trichoplusia ni (High 5). Examples of insect expression systems that can be used with the present invention, for example to produce NPC1L1 polypeptide, include Bac-To-Bac (Invitrogen Corporation, Carlsbad, Calif.) or Gateway (Invitrogen Corporation, Carlsbad, Calif.). If desired, deglycosylation enzymes can be used to remove carbohydrates attached during production in eukaryotic expression systems. The present invention includes both glycosylated and un-glycosylated canine, rabbit, hamster, cynomolgus monkey and rhesus monkey NPC1L1.

Other modifications may also include addition of aliphatic esters or amides to the polypeptide carboxyl terminus. The present invention also includes analogs of the NPC1L1 polypeptides which contain modifications, such as incorporation of unnatural amino acid residues, or phosphorylated amino acid residues such as phosphotyrosine, phosphoserine or phosphothreonine residues. Other potential modifications include sulfonation, biotinylation, or the addition of other moieties. For example, the NPC1L1 polypeptides of the invention may be appended with a polymer which increases the half-life of the peptide in the body of a subject. Subitable polymers include polyethylene glycol (PEG) (e.g., PEG with a molecular weight of 2 kDa, 5 kDa, 10 kDa, 12 kDa, 20 kDa, 30 kDa and 40 kDa), dextran and monomethoxypolyethylene glycol (mPEG).

The peptides of the invention may also be cyclized. Specifically, the amino- and carboxy-terminal residues of an NPC1L1 polypeptide or two internal residues of an NPC1L1 polypeptide of the invention can be fused to create a cyclized peptide. Methods for cyclizing peptides are conventional and very well known in the art; for example see Gurrath, et al., (1992) Eur. J. Biochem. 210:911-921.

The present invention contemplates any superficial or slight modification to the amino acid or nucleotide sequences which correspond to the NPC1L1 polypeptides of the invention. In particular, the present invention contemplates sequence conservative variants of the nucleic acids which encode the polypeptides of the invention. “Sequence-conservative variants” of a polynucleotide sequence are those in which a change of one or more nucleotides in a given codon results in no alteration in the amino acid encoded at that position. Function-conservative variants of the polypeptides of the invention are also contemplated by the present invention. “Function-conservative variants” are those in which one or more amino acid residues in a protein or enzyme have been changed without altering the overall conformation and function of the polypeptide, including, but, by no means, limited to, replacement of an amino acid with one having similar properties. Amino acids with similar properties are well known in the art. For example, polar/hydrophilic amino acids which may be interchangeable include asparagine, glutamine, serine, cysteine, threonine, lysine, arginine, histidine, aspartic acid and glutamic acid; nonpolar/hydrophobic amino acids which may be interchangeable include glycine, alanine, valine, leucine, isoleucine, proline, tyrosine, phenylalanine, tryptophan and methionine; acidic amino acids which may be interchangeable include aspartic acid and glutamic acid and basic amino acids which may be interchangeable include histidine, lysine and arginine.

The present invention includes polynucleotides encoding canine, hamster, rabbit, rhesus monkey and cynomolgus monkey NPC1L1 and fragments thereof as well as nucleic acids which hybridize to the polynucleotides. Preferably, the nucleic acids hybridize under low stringency conditions, more preferably under moderate stringency conditions and most preferably under high stringency conditions. A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength (see Sambrook, et al., supra). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. In an embodiment of the invention, low stringency hybridization conditions are 55° C., 5×SSC, 0.1% SDS, 0.25% milk, and no formamide at 42° C.; or 30% formamide, 5×SSC, 0.5% SDS at 42° C. In an embodiment of the invention, moderate stringency hybridization conditions are similar to the low stringency conditions except the hybridization is carried out in 40% formamide, with 5× or 6×SSC at 42° C. In an embodiment of the invention, high stringency hybridization conditions are similar to low stringency conditions except the hybridization conditions are carried out in 50% formamide, 5× or 6×SSC and, optionally, at a higher temperature (e.g., higher than 42° C.: 57° C., 59° C., 60° C., 62° C., 63° C., 65° C. or 68° C.). In general, SSC is 0.15M NaCl and 0.015M Na-citrate.

In an embodiment of the invention, low stringency hybridization conditions comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH₂PO₄H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.1% SDS, 5×Denhardt's reagent (50×Denhardt's contains per 500 ml:05 g Ficoll (Type 400, Pharmacia):05 g BSA (Fraction V; Sigma)) and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 1×SSPE, 0.1% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.

In an embodiment of the invention, medium stringency conditions comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH₂PO₄H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS, 5×Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 5.0×SSPE, 1.0% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.

In an embodiment of the invention, high stringency conditions comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH₂PO₄H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS, 5×Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 5-10×SSPE, 1.0% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.

Hybridization requires that the two nucleic acids contain complementary sequences, although, depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the higher the stringency under which the nucleic acids may hybridize. For hybrids of greater than 100 nucleotides in length, equations for calculating the melting temperature have been derived (see Sambrook, et al., supra, 9.50-9.51). For hybridization with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook, et al., supra).

In an embodiment of the invention, a polynucleotide of the invention (e.g., SEQ ID NO: 1, 3, 5, 7, or 9 or any polynucleotide that hybridizes thereto under any condition, for example, high stringency conditions e.g., as set forth herein) encodes a polypeptide that exhibits the ability to bind to ezetimibe or any structurally related compound (e.g., any of compounds 1-9 herein). The scope of the invention also includes any such polypeptide.

Also included in the present invention are polynucleotides comprising nucleotide sequences and polypeptides comprising amino acid sequences which are at least about 70% identical, preferably at least about 80% identical, more preferably at least about 90% identical and most preferably at least about 95% identical (e.g., 95%, 96%, 97%, 98%, 99%, 100%) to the reference canine, hamster, rabbit, rhesus monkey, or cynomolgus monkey NPC1L1 nucleotide (e.g., any of SEQ ID NOs: 1, 3, 5, 7, or 9) or amino acid sequences (e.g., SEQ ID NOs: 2, 4, 6, 8, or 10) when the comparison is performed by a BLAST algorithm wherein the parameters of the algorithm are selected to give the largest match between the respective sequences over the entire length of the respective reference sequences. Polypeptides comprising amino acid sequences which are at least about 70% similar or homologous, preferably at least about 80% similar or homologous, more preferably at least about 90% similar or homologous and most preferably at least about 95% similar or homologous (e.g., 95%, 96%, 97%, 98%, 99%, 100%) to the reference canine, hamster, rabbit, rhesus monkey, or cynomolgus monkey NPC1L1 (e.g., SEQ ID NOs: 2, 4, 6, 8 or 10), when the comparison is performed with a BLAST algorithm wherein the parameters of the algorithm are selected to give the largest match between the respective sequences over the entire length of the respective reference sequences, are also included in the present invention.

Sequence identity refers to exact matches between the nucleotides or amino acids of two sequences which are being compared. Sequence similarity or homology refers to both exact matches between the amino acids of two polypeptides which are being compared in addition to matches between nonidentical, biochemically related amino acids. Biochemically related amino acids which share similar properties and may be interchangeable are discussed above.

In an embodiment of the invention, a polypeptide of the invention (e.g., SEQ ID NO: 2, 4, 6, 8 or 10 or any polypeptide bearing similarity or identity thereto e.g., 95% or more, including 97% or 99%) exhibits the ability to bind to ezetimibe or any structurally related compound (e.g., any of compounds 1-9 herein). The scope of the invention also includes any polynucleotide encoding such a polypeptide.

The following references regarding the BLAST algorithm are herein incorporated by reference: BLAST ALGORITHMS: Altschul, S. F., et al., (1990) J. Mol. Biol. 215:403-410; Gish, W., et al., (1993) Nature Genet. 3:266-272; Madden, T. L., et al., (1996) Meth. Enzymol. 266:131-141; Altschul, S. F., et al., (1997) Nucleic Acids Res. 25:3389-3402; Zhang, J., et al., (1997) Genome Res. 7:649-656; Wootton, J. C., et al., (1993) Comput. Chem. 17:149-163; Hancock, J. M., et al., (1994) Comput. Appl. Biosci. 10:67-70; ALIGNMENT SCORING SYSTEMS: Dayhoff, M. O., et al., “A model of evolutionary change in proteins.” in Atlas of Protein Sequence and Structure, (1978) vol. 5, suppl. 3. M. O. Dayhoff (ed.), pp. 345-352, Natl. Biomed. Res. Found., Washington, D.C.; Schwartz, R. M., et al., “Matrices for detecting distant relationships.” in Atlas of Protein Sequence and Structure, (1978) vol. 5, suppl. 3.” M. O. Dayhoff (ed.), pp. 353-358, Natl. Biomed. Res. Found., Washington, D.C.; Altschul, S. F., (1991) J. Mol. Biol. 219:555-565; States, D. J., et al., (1991) Methods 3:66-70; Henikoff, S., et al., (1992) Proc. Natl. Acad. Sci. USA 89:10915-10919; Altschul, S. F., et al., (1993) J. Mol. Evol. 36:290-300; ALIGNMENT STATISTICS: Karlin, S., et al., (1990) Proc. Natl. Acad. Sci. USA 87:2264-2268; Karlin, S., et al., (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877; Dembo, A., et al., (1994) Ann. Prob. 22:2022-2039; and Altschul, S. F. “Evaluating the statistical significance of multiple distinct local alignments.” in Theoretical and Computational Methods in Genome Research (S. Suhai, ed.), (1997) pp. 1-14, Plenum, New York.

Protein Purification

The proteins, polypeptides and antigenic fragments of this invention can be purified by standard methods, including, but not limited to, salt or alcohol precipitation, affinity chromatography (e.g., used in conjunction with a purification tagged NPC1L1 polypeptide as discussed above), preparative disc-gel electrophoresis, isoelectric focusing, high pressure liquid chromatography (HPLC), reversed-phase HPLC, gel filtration, cation and anion exchange and partition chromatography, and countercurrent distribution. Such purification methods are well known in the art and are disclosed, e.g., in “Guide to Protein Purification”, Methods in Enzymology, Vol. 182, M. Deutscher, Ed., 1990, Academic Press, New York, N.Y.

Purification steps can be followed by performance of assays for receptor binding activity as described below. Particularly where an NPC1L1 polypeptide is being isolated from a cellular or tissue source, it is preferable to include one or more inhibitors of proteolytic enzymes in the assay system, such as phenylmethanesulfonyl fluoride (PMSF), Pefabloc SC, pepstatin, leupeptin, chymostatin and EDTA.

In an embodiment of the invention, canine, hamster, rabbit, cynomolgus monkey or rhesus monkey NPC1L1 is purified by isolating a cell membrane comprising the polypeptide from other contents of a host cell. For example, the cell carrying the NPC1L1 polypeptide can be lysed and the membranes from the cell can be pelleted by centrifugation.

NPC1L1

The present invention includes canine, hamster, rabbit, cynomolgus monkey or rhesus monkey NPC1L1 polypeptides and polynucleotides as set forth below along with allelic variants and fragments thereof (e.g., antigenic fragments thereof).

Canine NPC1L1 ORF (SEQ ID NO: 1) atggcggaca ctggcctgag gggctggctg ctatgggcac tgctcctgca tgtggcccag 60 agtgagctgt acacacccat ccaccagcct ggctactgcg ctttctacga cgagtgtggg 120 aagaacccag agctgtctgg gggactggcg cctctgtcta atgtgtcctg cctgtccaac 180 acgcccgccc tccgtgtcac tggtgagcac ctgaccctcc tacagcgcat ctgcccccgc 240 ctctacacgg gcaccaccac ctatgcctgc tgctccccca agcagctgct gtccctggag 300 acgagcctgg cggtcaccaa ggccctcctc acccgctgcc ccacctgctc cgacaacttt 360 gtgaacctgc actgccaaaa cacctgcagc cccaaccaaa gtctcttcat caacgtgacc 420 cgcgtggctg ggggcggggg tggccggccc caggctgtgg tggcctatga ggccttctac 480 caggacacct ttgcccagca gacctacgac tcttgcagcc gggtgcgcat ccctgcggct 540 gccacgctgg ccgtgggcac catgtgtggc gtttatggct ccaccctctg caatgctcag 600 cgctggctca atttccaggg ggacacttcg aatggcctgg ctcccctaga catcaccttc 660 cacctgatgg agcccggcca ggccctaggg agtgggatgc aggctctgac cggggagatc 720 aggccctgca acgagtccca gggcaatggc acggtggcct gctcctgcca ggactgtgct 780 gcgtcctgcc ccaccatccc ccagccccag gcactggact ccaccttcta cctgggcggg 840 ctggaaggtg ggctggccct tgtcatcatc ctctgctctg cttttgccct gcttaccacc 900 ttcctggtgg gtacccgcct ggcctcctcc tgtggcaagg acaagacgcc agaccccaag 960 gcaggcatga gcctgtctga caaactcagc ctctccacca acgtcatcct tagccagtgc 1020 ttccagaact ggggcacatg ggtggcctca tggccgctga ccatcctgtt ggtgtccatc 1080 gccgtggtat tggccttgtc aggaggcctg gcctttgtgg aactgaccac ggacccagtg 1140 gagctgtggt cggcccccag cagccaagcc cggagtgaga aggctttcca cgaccagcat 1200 tttggcccct tcctccgaac caaccaggtg atcttgacgg ctcccaaccg gcccagctac 1260 cactacgact ccctgctcct ggggcccaag aacttcagtg gggtcctggc ctctgacctc 1320 ctgctggagc tgctggagct acaggagacG ctgcggcacc tccaggtgtg gtcgcccgag 1380 gagcagcgcc acatctcgct gcaggacatc tgcttcgcgc ccctcaaccc tcacaatgcc 1440 agcctctccg actgctgcat caacagcctc ctgcagtatt tccagagcaa ccgcacgcac 1500 ctgctgctca cggccaacca gacgctgacg ggccagacct cccaggtgga ctggagggac 1560 cactttctct actgtgctaa cgccccactc accttcaagg atggcacagc cctagccctg 1620 agctgcatgg ctgactatgg gggccctgtc ttccccttcc ttgccgtggg tggctacaaa 1680 gggaaggact actctgaggc ggaggccctg attatgacct tctccctcaa caactatgcc 1740 cctggggacc cccggctggc ccaggctaag ctctgggagg cagccttctt ggaggagatg 1800 aaagccttcc agcggcggac agctggcact ttccaggtca cattcatggc tgagcgctcc 1860 ctggaggacg agattaaccg cacgacggcg gaggacctcc ccatcttcgg agtcagctac 1920 atcatcatct tcctgtacat ctccctggcg ctgggcagct actccagctg gcgccgggtg 1980 ccggtggact ccaaggtcac gctgggcctg ggcggggtgg cggtggtgct gggagcagtg 2040 acagcggcca tgggcttctt ctcctacctc ggcgtgccgt cctccctggt gatccttcag 2100 gtggtgcctt tcctggtgtt ggccgtgggc gctgacaaca tcttcatctt tgttctggag 2160 taccagaggc tgccccggag gccgggagag ccgcgggagg cccacatcgg ccgagcgctg 2220 ggcagtgtgg cccctagcat gttgctctgc agcctgtctg aggccatctg cttctttcta 2280 ggggccctga cccctatgcc cgctgtgaag acctttgccc tgatctcggg ctttgccatc 2340 gtcctggact tcttgctgca ggtgtcagcc tttgtggctc tgctttctct ggacagcagg 2400 aggcaggagg cctcccgctt ggacgtctgc tgctgcgtga gcgccccgaa gctgcctgca 2460 cccggccaga gcgagggact cctgcttcga gtcttccgca agttctacgt cccagtcctg 2520 ctgcaccggg tgacacgggc ggtggtgctg ctgctgttca ccggcctctt cggggtgggg 2580 ctctacttca tgtgccacat ccgcgtggga ttggatcagg agctggccct gcccaaggac 2640 tcatacctgc tggactattt cttcttcctg aaccgctact ttgaggtggg ggctcccgtc 2700 tactttgtca ccacgggagg ctacaacttc tccagcgagg cgggcatgaa tgctgtgtgc 2760 tccagtgccg ggtgcgacag ttactcctta acccagaaga tccagtacgc caccgagttc 2820 cccgaggagt cttacctggc catccctgcc tcctcctggg tggatgactt catcgactgg 2880 ctgaccccgt cctcctgctg ccgcctttat gcctttggtg ctaataagga caaattctgc 2940 ccttcgactg tcaactccct agcctgcttg aagaactgcg tgaacttcac actgggccct 3000 gtccggccat ccgtggacca gttccacaag taccttccct ggttcctgag tgacccgccc 3060 aacatcaagt gtcccaaagg tgggctggca gcgtacaaca cctccgtgca tttgggatct 3120 gatggccagg ttttagcctc ccggttcatg gcctaccaca agccgctgcg gaactcggag 3180 gattacactg aggccctgcg ggtgtcacgg gcgctggcgg ccaacatcac ggcccagctg 3240 cggcaggtgc caggcaccga cccggccttc gaggtcttcc cctacacgat caccaacgtg 3300 ttctacgagc agtacctgag cgtggtcccc gagggcctct tcatgctcgc catctgcctg 3360 ctgcccacct tcgtagtctg ctgcctgctg ctgggcatgg acctacgctc cggcctcctc 3420 aacctgttct ccatcgtcat gatcctcgtg gacaccgtgg gcttcatggc cctgtggggc 3480 atcagttaca atgccgtgtc gctcatcaac ctggtcacgg cggtgggcat ctccgtggag 3540 tttgtgtccc acatcacccg ctcctttgca gtcagcaccc ggcccacccg gctggagagg 3600 gccaaggagg ccaccatctc catgggcagc gcggtgtttg ctggcgtggc catgaccaac 3660 ctgccgggca tcctcgtcct gggcctggcc aaggcacagc tcatccagat cttcttcttc 3720 cgcctcaacc tcctcatcac cgtgctgggt ctgctgcatg gcctggtctt cctgccagtg 3780 gtcctcagct acctcgggcc tgatatcaat gcagctctcg tgctggacca gaagaagaca 3840 gaagaggcca tcggggcccc tgcccacctg gtcccaacat ccacggccag cagcacctat 3900 gtcaactacg gcttccaaca tcccgccaac ggtgtagtgg gcgacagttc tctgccccgc 3960 agtggaccgg acctctga 3978 (SEQ ID NO: 2)    1 MADTGLRGWL LWALLLHVAQ SELYTPIHQP GYCAFYDECG KNPELSGGLA   51 PLSNVSCLSN TPALRVTGEH LTLLQRICPR LYTGTTTYAC CSPKQLLSLE  101 TSLAVTKALL TRCPTCSDNF VNLHCQNTCS PNQSLFINVT RVAGGGGGRP  151 QAVVAYEAFY QDTFAQQTYD SCSRVRIPAA ATLAVGTMCG VYGSTLCNAQ  201 RWLNFQGDTS NGLAPLDITF HLMEPGQALG SGMQALTGEI RPCNESQGNG  251 TVACSCQDCA ASCPTIPQPQ ALDSTFYLGG LEGGLALVII LCSAFALLTT  301 FLVGTRLASS CGKDKTPDPK AGMSLSDKLS LSTNVILSQC FQNWGTWVAS  351 WPLTILLVSI AVVLALSGGL AFVELTTDPV ELWSAPSSQA RSEKAFHDQH  401 FGPFLRTNQV ILTAPNRPSY HYDSLLLGPK NFSGVLASDL LLELLELQET  451 LRHLQVWSPE EQRHISLQDI CFAPLNPHNA SLSDCCINSL LQYFQSNRTH  501 LLLTANQTLT GQTSQVDWRD HFLYCANAPL TFKDGTALAL SCMADYGGPV  551 FPFLAVGGYK GKDYSEAEAL IMTFSLNNYA PGDPRLAQAK LWEAAFLEEM  601 KAFQRRTAGT FQVTFMAERS LEDEINRTTA EDLPIFGVSY IIIFLYISLA  651 LGSYSSWRRV PVDSKVTLGL GGVAVVLGAV TAAMGFFSYL GVPSSLVILQ  701 VVPFLVLAVG ADNIFIFVLE YQRLPRRPGE PREAHIGRAL GSVAPSMLLC  751 SLSEAICFFL GALTPMPAVK TFALISGFAI VLDFLLQVSA FVALLSLDSR  801 RQEASRLDVC CCVSAPKLPA PGQSEGLLLR VFRKFYVPVL LHRVTRAVVL  851 LLFTGLFGVG LYFMCHIRVG LDQELALPKD SYLLDYFFFL NRYFEVGAPV  901 YFVTTGGYNF SSEAGMNAVC SSAGCDSYSL TQKIQYATEF PEESYLAIPA  951 SSWVDDFIDW LTPSSCCRLY AFGANKDKFC PSTVNSLACL KNCVNFTLGP 1001 VRPSVDQFHK YLPWFLSDPP NIKCPKGGLA AYNTSVHLGS DGQVLASRFM 1051 AYHKPLRNSE DYTEALRVSR ALAANITAQL RQVPGTDPAF EVFPYTITNV 1101 FYEQYLSVVP EGLFMLAICL LPTFVVCCLL LGMDLRSGLL NLFSIVMILV 1151 DTVGFMALWG ISYNAVSLIN LVTAVGISVE FVSHITRSFA VSTRPTRLER 1201 AKEATISMGS AVFAGVAMTN LPGILVLGLA KAQLIQIFFF RLNLLITVLG 1251 LLHGLVFLPV VLSYLGPDIN AALVLDQKKT EEAIGAPAHL VPTSTASSTY 1301 VNYGFQHPAN GVVGDSSLPR SGPDL* Rabbit NPC1L1 ORF (SEQ ID NO: 3) atggcagggg ctgcgcgggg ctggctgctc tgggccctgc tcctgcacca ggcccaggca 60 gagctgtaca cgcccgtgca ccaggccggc tactgcgcct tctacgagga gtgcgggaag 120 aaccctgagc tgtctggggg cctcacatcg ctgtccaacg tgtcctgcct gtccaacacg 180 cctgcccgcc atgtcacggg cgaccacctg gccctcctgg agcgcatctg cccccgcctc 240 tacaacggcc ccaacaccac ctacgcctgc tgctcgccca ggcagctggt gtcgctggag 300 accagcatgt ccgtcaccaa ggccctgctc acgcgctgcc ccgcctgctc tgacaacttc 360 gtgagcctgc actgccagaa cacctgcagc ccggaccaga gcctcttcat caacgtgacg 420 cgcgtggtct cccagggcgc tgggcagctc caggccgtcg tggcctacga ggcctactac 480 gagcgcagct tcgccgagcg ggcctacgag tcctgcagcc gcgtgcgcat ccccgccgcc 540 gccacgctgg ccgtgggcag catgtgcggc gtgtacggct ctgccctctg caacgcccag 600 cgctggctca acttccaggg ggacacgagc aacggcctgg ccccgctgga cattaccttc 660 cacctgcggg agcccgggca ggcgccgggc agcgggatgc aactgctgaa cgcggagatc 720 gcgccctgca acgagtccca ggacagcgcc gcggcctgct cctgccagga ctgtgccgcg 780 tcctgcccgg ccatcacgca gcctgaggcc ctggactcct ccttccgcat tggccgcgtg 840 cggggtgggg tggcactcgt cgtcatcctc tgcagcaccc tgggcgtgct cctcctgggc 900 ctcgtgtgcg cccgcaggta ctcggccaag gccaggggca cggcgacggc ccccacggcc 960 tgctccaggc tctcccaccg catcagcctg tccatccaca ccttcctcca tcggctcttc 1020 cagtgctggg gcacgtgggt ggcctcgtgg cccctgacca tcctggccgt gtccatcgcg 1080 gtcgtggtgt ccttggcgtg tggcctggcc ttcacggagc tcacaacgga ccccgtggag 1140 ctgtggtcgg cccccaacag ccaagcccgc agcgagaagg ctttccacga ccagcacttc 1200 ggccccttct tccgaacgaa ccaggtgatc ctgacggcgc ctacccgctc ccgctacact 1260 tacaactccc tgctgctggg gccccggaac ttcagtggga tcctggccat ggacctgctg 1320 ctggagctac tggagctgca ggagcggctg cgggccctgc aggtgtggtc gcccgaggcg 1380 cagcgcaacg tgagcctgcg ggacgtctgc tacgccccgc tcaacccgca caacgccagc 1440 ctcaccgact gctgtatcaa cagcctgctg cagtacttcc agaacaaccg cacgctgctg 1500 cagctcacgg ccaaccagac gctcctgggc cagactgccc aggtcgactg gagggaccac 1560 tttctctact gtgccaatgc ccccctcacc ttccaagacg gcacggccct gtccctgagc 1620 tgcatggccg actacggggc gcccgtcttc cctttcctcg ccgttggggg atacgaaggc 1680 gaggactact cggatgcgga ggccctcatc ttaaccttct ccctcaacaa ctaccctgcg 1740 ggggaccccc gcctggccca ggtcaagctc tgggaggagg ccttcgtgaa ggagatgcga 1800 gccttgcagc ttgggaagtc cagcaaattc caggtcacgt tcatggccga gcgctccctg 1860 gaggatgaga tcaaccgcac cacggctgag gacctgccca tctttgccat cagctacatc 1920 gtcaccttcc tgtacatcgc cctggccctg ggccgctact ccagctggcg ccgattgccg 1980 gtggactcca agatcacgct gggcctgggc ggggtggtca tggtgctgag cgcggtcatg 2040 gcttccatgg gcttcttctc ctacctgggc atcccgtcgt ccctgatcat cctgcaagtg 2100 gtgcctttcc tggtgctggc cgtgggggcc gacaacatct tcatcctcgt tctcgagtac 2160 cagcggctgc cgcggaggcc tgaggagtcg cgggaggccc acatcggccg agccctgggc 2220 agggtggctc ccagcatgct gctgtgcagc ctctccgaga ccatctgctt cttcctgggg 2280 gccctgaccc ccatgccagc cgtgcgtacc tttgccctga cgtctggcct ggcggtgcaa 2340 ctcgacttcc tgctgcagat gactgccttc gtggccctgc tgtccctgga cagcaagagg 2400 caggaggctt cccggccaga tgtgtgctgc tgcctggagc cccggaagct gccctcccag 2460 cagcagagcg aggggctgct gctgtgtttc ttccgcaaag tctacgcccc gctcctgctg 2520 cacaaggtca cccgcgtggt cgtgctgctg ctctttctgt tcctgttcgg atcgagtctc 2580 tacttcatgt gccaggtcac cgtggggctg gaccaggage tggccctgcc caaggactcg 2640 tacctgatcg actacttcct gtttctgaac cgctactttg aggtgggggc cccagtgtac 2700 tttgtcacca cctcgggcta caacttctcc agcgaggcgg gcatgaacgc catctgctcc 2760 agcgcaggct gcgacagctt ctccctcacc cagaagatcc aatacgccac cgagttcccc 2820 gagcagtctt acctggccat ccccgcctcc tcctgggtgg acgacttcat cgactggcta 2880 accccgtcct cctgctgccg cctttacatc ctcggcccca ataaggacga gttctgcccc 2940 tccacagtca actccttgaa ctgcctgagg aattgcatga gcttgacgct gggccctgtg 3000 cggccctcgg tggagcagtt ccacaagtac ctgccctggt ttctgaatga cccccccaac 3060 atccgatgtc ccaagggtgg cctggcggcg tacagcacct ctgtgaacct gagcgccgat 3120 ggccagattg tagccacccg cttcatggcc taccacaagc cgctgaagaa ctcgcaggac 3180 tacaccgagg ccctgcgggc gtcgcgggag ctggcggcca acatcaccgc gagcctgcgg 3240 caggtgccgg gcacggaccc cgccttcgag gtcttcccct acacgatctc caacgtgttc 3300 tacgagcagt acctgaccgt gctcccggag gggctcgcca cgctcggcct ctgcctcgtg 3360 cccaccttcg tcgtctgctg cctcctgctg ggcctggacc tgcgctccgg cctcctcaac 3420 ctgctgacca tcgtcatgat tctcgtggac accgtgggcc tcatgacgct gtggagcatc 3480 agctacaacg ccgtgtccct catcaatctg gtcacggcgg tgggcatgtc cgtggagttc 3540 gtgtcccaca tcacccgctc ctttgccgtc agcaccaagc ccagccggct ggagagagcc 3600 aaggaggcca ccatctccat gggcagtgcg gtgtttgcag gggtggccat gaccaacctg 3660 ccgggcatcc tcatcctggg cctcgccaag gcccagctca tccagatctt cttcttccgc 3720 ctcaacctcc tcatcaccct gctggggctg ctgcacggcc tggtcttcct gcccgtcatc 3780 ctcagctacc ttgggcctga cgtcaacccg gctctggttg ctctggagcg gacgcgagcc 3840 caggaggcgg ctgacgctgc ggcgggctcc tgcccaaatc accccgaccc tacctccaac 3900 atctacgtca actccggctt tgacgaggca gccagggatg tcggcagctc tgcccccacc 3960 agaaagcaga agttctga 3978 (SEQ ID NO: 4)    1 MAGAARGWLL WALLLHQAQA ELYTPVHQAG YCAFYEECGK NPELSGGLTS   51 LSNVSCLSNT PARHVTGDHL ALLERICPRL YNGPNTTYAC CSPRQLVSLE  101 TSMSVTKALL TRCPACSDNF VSLHCQNTCS PDQSLFINVT RVVSQGAGQL  151 QAVVAYEAYY ERSFAERAYE SCSRVRIPAA ATLAVGSMCG VYGSALCNAQ  201 RWLNFQGDTS NGLAPLDITF HLREPGQAPG SGMQLLNAEI APCNESQDSA  251 AACSCQDCAA SCPAITQPEA LDSSFRIGRV RGGVALVVIL CSTLGVLLLG  301 LVCARRYSAK ARGTATAPTA CSRLSHRISL SIHTFLHRLF QCWGTWVASW  351 PLTTLAVSIA VVVSLACGLA FTELTTDPVE LWSAPNSQAR SEKAFHDQHF  401 GPFFRTNQVI LTAPTRSRYT YNSLLLGPRN FSGILAMDLL LELLELQERL  451 RALQVWSPEA QRNVSLRDVC YAPLNPHNAS LTDCCINSLL QYFQNNRTLL  501 QLTANQTLLG QTAQVDWRDH FLYCANAPLT FQDGTALSLS CMADYGAPVF  551 PFLAVGGYEG EDYSDAEALI LTFSLNNYPA GDPRLAQVKL WEEAFVKEMR  601 ALQLGKSSKF QVTFMAERSL EDEINRTTAE DLPIFAISYI VTFLYIALAL  651 GRYSSWRRLP VDSKITLGLG GVVMVLSAVM ASMGFFSYLG IPSSLIILQV  701 VPFLVLAVGA DNIFILVLEY QRLPRRPEES REAHIGRALG RVAPSMLLCS  751 LSETICFFLG ALTPMPAVRT FALTSGLAVQ LDFLLQMTAF VALLSLDSKR  801 QEASRPDVCC CLEPRKLPSQ QQSEGLLLCF FRKVYAPLLL HKVTRVVVLL  851 LFLFLFGSSL YFMCQVTVGL DQELALPKDS YLIDYFLFLN RYFEVGAPVY  901 FVTTSGYNFS SEAGMNAICS SAGCDSFSLT QKIQYATEFP EQSYLAIPAS  951 SWVDDFIDWL TPSSCCRLYI LGPNKDEFCP STVNSLNCLR NCMSLTLGPV 1001 RPSVEQFHKY LPWFLNDPPN IRCPKGGLAA YSTSVNLSAD GQIVATRFMA 1051 YHKPLKNSQD YTEALRASRE LAANITASLR QVPGTDPAFE VFPYTISNVF 1101 YEQYLTVLPE GLATLGLCLV PTFVVCCLLL GLDLRSGLLN LLTIVMILVD 1151 TVGLMTLWSI SYNAVSLINL VTAVGMSVEF VSHITRSFAV STKPSRLERA 1201 KEATISMGSA VFAGVAMTNL PGILILGLAK AQLIQIFFFR LNLLITLLGL 1251 LHGLVFLPVI LSYLGPDVNP ALVALERTRA QEAADAAAGS CPNHPDPTSN 1301 IYVNSGFDEA ARDVGSSAPT RKQKF* Hamster NPC1L1 ORF (SEQ ID NO: 5) atggcagctg gcctacagag atggctgctc tgggccctac tcctgaatgc ggcccggggt 60 gagatacaca cacccattca taaagctggc gtctgtacct tctatgaaga gtgtgggaag 120 aacccagagc tgtccggagg cctcacgtca ctgtccaatg tatcttgcct gtctaacacc 180 ccagcccgcc gtgtcacagg tgaccacctg accctccttc agcgcatctg cccccgcctg 240 tacaatggcc ccaacaatac ctatgcttgt tgctccgccc agcagctagt ggcattagaa 300 aagagcatgt ctatcaccaa ggccctcctc acccgctgcc cagcctgctc tgacaatttt 360 gtgagcttgc actgccacaa cacctgcagc cctgaccaga gcctcttcat caatgtcacc 420 cgtgtggttg agcaggcgga ccctcagcag cctccagctg tggtggccta tgaagccttt 480 taccagagca gctttgcaga gaaggcctat gagtcctgta gccgggtacg catccccgcg 540 gctgcctcac tggctgtggg caccatgtgt ggggtgtatg gctctgccct gtgcaatgcc 600 caacgctggc tcaacttcca gggagacaca gggaacggcc tggctcctct cgacatcacc 660 ttccacctcg tggagtccgg ccaggccctg ccagatggga tgcagcctct gaatggggag 720 atcacgccct gcaatcagtc ggagggtgta gagtcggctg cctgttcctg ccaggactgt 780 gcagcgtctt gccctgtcat tccgcagccc tcagccctgc ccccttcctt ctacatgggt 840 aaaatgcctg gctggctggc tctcatcatc atcttctgtg cggtcttcgt gctgctcaca 900 gctgtcctta tatatcttcg agtggtttcc aataggagca ggagcaagaa aacaggcctc 960 caggaagccc cgaaccgccc tcctaagcgc agattctcac ctcacatcgt ccttggccgg 1020 tttttccaga gctggggcac aagagtggcc tcatggccac tcactgtctt ggcgctgtcc 1080 tttatggttg tgatagcctt gtcagtgggc atgacctaca tagaactcac cacagaccct 1140 gtggaactgt ggtcagcccc caaaagccaa gctcggaaag agaaggcttt ccacgacgag 1200 cattttggcc ccttcttccg aaccaaccag gtttttgtga cagctcggaa caggtccagc 1260 tatagatatg actccctgct gctagggccc aagaacttca gtgggctcct gtccctggac 1320 ctggtgctgg agctgctgga gctccaagag aggcttcgac acctgcaggt gtggtcccct 1380 gaggcacagc gcaacatctc cctgcaggac atctgctatg cccccctcaa accgcacaac 1440 accagcctct ccgactgctg tgtcaacagt ctccttcagt acttccagaa caaccgcacg 1500 ctcctgctgc tcacagccaa ccagacgctc aatggccaga cttccctggt ggactggagg 1560 gaccacttcc tctactgtgc aaatgcgcct ctcacgttca aagacggcac gtctctggcc 1620 ctgagctgca tcgcggacta tggggcccct atcttcccct tccttgctgt cggggggtac 1680 caagggacgg actactctga ggcagaggcg ctgatcataa ctttctctct caataactac 1740 cctgctgatg atccccgcat ggcccaggcc aagctctggg aggaggcttt tctgaaggaa 1800 atgcaagcct tccagagcag tgtggctgac aagttccagg ttgcattctc agctgagcgc 1860 tctctggagg atgagatcaa ccgcaccacc atccaggacc tgcctgtctt cgccatcagc 1920 tacattatcg tcttcctgta catctctctg gccctgggca gctactccaa atggaagcga 1980 gtagcggtgg attccaaggc tactctgggc ctcggtgggg tggctgtcgt gctgggagca 2040 gtcgtggctg ccatgggttt ctactcctac ctgggtgttc cctcctcact ggttatcatc 2100 caagtggtgc ctttcctggt gctggccgtg ggagctgaca acatcttcat ctttgttctt 2160 gagtaccaga ggctgcctag gaggcctggg gageagegag aggcccacat cggccgtacc 2220 ctgggcagtg tggcccccag catgctgctg tgcagcctct ctgaggctgt ctgcttcttt 2280 ctaggggccc tgacccccat gccagctgtg aggacctttg ccttgaccgc tggcctttcg 2340 attatcctcg acttcctgct ccagatgact gccttcgtgg ccctgctctc cctggatagc 2400 aagaggcagg aggcctctcg ccccgacatc ttatgctgtc tttcaccccg gaaactaccc 2460 ccacctgaac agcaagaggg gctcttactc cgcttcttca gaaagatata tgctcccttc 2520 ctgctgcaca ggttcatccg ccctgttgtg ctgctgctgt ttctggccct gtttggagca 2580 aatctctact taatgtgcca catcagcgtg gggttggacc aggagctggc cctgcctaag 2640 gattcctact tgattgacta cttcctcttt ttgaaccgat actttgaggt ggggcctccc 2700 gtgtactttg tcaccacctc gggttacaac ttctccagcg aggcaggcat gaatgccatt 2760 tgctctagtg caggctgtga cagcttctcc atgacccaga agatccaata tgccactgaa 2820 ttccctgagc agtcttacat agggattgct gcatcctcct gggtagacga cttcatcgac 2880 tggctgaccc cgtcctcctg ctgccgcctt tatatctttg gccccaatac gggtgacttc 2940 tgtccttcaa ctgatacttc cttgagctgt ctaaaaaact gcatgaactt cactctgggc 3000 cccgtgaggc ccacagcaga acagtttcac aagtatctgc cctggttcct ggacgatcca 3060 cccaacatca gatgccccaa agggggtctg gcagcatata gaacttccgt gaatttgagc 3120 tcagatggcc agattatago ctcccagttc atggcctacc acaagccgct caggaactca 3180 caggacttca cagaagctct ccggacatcc cgattgctgg cagccaacat cacagctgaa 3240 ctacggaaag tgcctggcac agccccagac tttgaggtct tcccctacac gatctccaac 3300 gtgttctacg agcagtacct gactgtcctc cccgagggca tcttcacact ggctctctgc 3360 ttcgtgccca ccttcgtcgt ctgctacctc ctgctgggcc tggacatgcg ctcaggcatc 3420 ctcaacctgc tctccatcat catgatcctt gtggacacca tcgggctcat ggctgtgtgg 3480 ggcatcagct acaatgctgt gtccctcatc aaccttgtca cggcagtggg aatgtctgtg 3540 gagttcgtgt cccacctcac ccggtccttt gctgtcagca ccaagcccac ccggctggag 3600 agggccaagg atgccaccgt ctccatgggc agtgcggtgt ttgctggcgt ggccatgacc 3660 aacttcccag gcatcctcat cctgggcttc gcccaggccc agctaatcca gatcttcttc 3720 ttccgcctca acctcctgat caccttgctg ggcctgctgc acggcctggt cttcctgccg 3780 gttgtcctca gctatctggg acccgatgtg aacccagagc tggtgctgga ggagaaacta 3840 gctacggagg cagcggtggc cccagagcct tccagcccga agtacccctt ccctgataat 3900 gactatgtta atcacagttt tgaggaagcc acccctggag ctgctgctgc tagtagctcc 3960 ttgcctaaaa gcggccaaaa gttttaa 3987 (SEQ ID NO: 6)    1 MAAGLQRWLL WALLLNAARG EIHTPIHKAG VCTFYEECGK NPELSGGLTS   51 LSNVSCLSNT PARRVTGDHL TLLQRICPRL YNGPNNTYAC CSAQQLVALE  101 KSMSITKALL TRCPACSDNF VSLHCHNTCS PDQSLFINVT RVVEQADPQQ  151 PPAVVAYEAF YQSSFAEKAY ESCSRVRIPA AASLAVGTMC GVYGSALCNA  201 QRWLNFQGDT GNGLAPLDIT FHLVESGQAL PDGMQPLNGE ITPCNQSEGV  251 ESAACSCQDC AASCPVIPQP SALPPSFYMG KMPGWLALII IFCAVFVLLT  301 AVLIYLRVVS NRSRSKKTGL QEAPNRPPKR RFSPHIVLGR FFQSWGTRVA  351 SWPLTVLALS FMVVIALSVG MTYIELTTDP VELWSAPKSQ ARKEKAFHDE  401 HFGPFFRTNQ VFVTARNRSS YRYDSLLLGP KNFSGLLSLD LVLELLELQE  451 RLRHLQVWSP EAQRNISLQD ICYAPLKPHN TSLSDCCVNS LLQYFQNNRT  501 LLLLTANQTL NGQTSLVDWR DHFLYCANAP LTFKDGTSLA LSCIADYGAP  551 IFPFLAVGGY QGTDYSEAEA LIITFSLNNY PADDPRMAQA KLWEEAFLKE  601 MQAFQSSVAD KFQVAFSAER SLEDEINRTT IQDLPVFAIS YIIVFLYISL  651 ALGSYSKWKR VAVDSKATLG LGGVAVVLGA VVAAMGFYSY LGVPSSLVII  701 QVVPFLVLAV GADNIFIFVL EYQRLPRRPG EQREAHIGRT LGSVAPSMLL  751 CSLSEAVCFF LGALTPMPAV RTFALTAGLS IILDFLLQMT AFVALLSLDS  801 KRQEASRPDI LCCLSPRKLP PPEQQEGLLL RFFRKIYAPF LLHRFIRPVV  851 LLLFLALFGA NLYLMCHISV GLDQELALPK DSYLIDYFLF LNRYFEVGPP  901 VYFVTTSGYN FSSEAGMNAI CSSAGCDSFS MTQKIQYATE FPEQSYIGIA  951 ASSWVDDFID WLTPSSCCRL YIFGPNTGDF CPSTDTSLSC LKNCMNFTLG 1001 PVRPTAEQFH KYLPWFLDDP PNIRCPKGGL AAYRTSVNLS SDGQIIASQF 1051 MAYHKPLRNS QDFTEALRTS RLLAANITAE LRKVPGTAPD FEVFPYTISN 1101 VFYEQYLTVL PEGIFTLALC FVPTFVVCYL LLGLDMRSGI LNLLSIIMIL 1151 VDTIGLMAVW GISYNAVSLI NLVTAVGMSV EFVSHLTRSF AVSTKPTRLE 1201 RAKDATVSMG SAVFAGVAMT NFPGILILGF AQAQLIQIFF FRLNLLITLL 1251 GLLHGLVFLP VVLSYLGPDV NPELVLEEKL ATEAAVAPEP SSPKYPFPDN 1301 DYVNHSFEEA TPGAAAASSS LPKSGQKF* Rhesus Monkey NPC1L1 ORF (SEQ ID NO: 7) atggcggagg ccggcctgag gggctggctg ctgtgggccc tgctcctgca cttggcccag 60 agcgagcctt acacacccat ccaccagcct ggctactgcg ccttctatga cgaatgtggg 120 aagaacccag agctgtctgg aggcctcatg acactctcca acgtgtcctg tctgtccaac 180 acgccagccc gcaacatcac aggtgatcac ctgatcctat tacagaggat ctgcccccgc 240 ctctacaccg gccccaacac ccaagcctgc tgctccgcca agcagctggt atcattggaa 300 gcgagtctgt cgatcaccaa ggccctcctc acccgctgcc cagcctgctc tgacaatttc 360 gtgagcctgc actgccacaa cacatgcagc cccaaccaga gcctcttcat caatgtgacc 420 cgcgtggctc agctaggggc tggacaactc ccagctgtgg tggcctatga ggccttctac 480 cagcacagct ttgccgagca gagctatgac tcctgcagcc gtgtgcacat ccctgcggct 540 gccacgctgg ctgtgggcag catgtgtggc gtgtatggct ctgccctttg caatgcccag 600 cgctggctca acttccaggg agacacaggc aatggtctgg ccccactgga catcaccttc 660 cacctcttgg agcccggcca ggctgtgggg agtgggattc agcctctgaa tgagggggtt 720 gcacgttgca atgagtccca aggtgacgac gcagtggcct gctcctgcca ggactgtgct 780 gcatcctgtc ctgccatcgc ccatccccag gccctggact ccaccttccg cctgggccgg 840 atgccgggtg ggctggtcct catcatcatc ctctgttctg tcttcactgt ggtcgccatc 900 ctgctcgtgg gactccgtgt ggcccccacc agggacaaaa gcaagacggt ggaccccaag 960 aagggcacca gcctctctga taagctcagc ttctccaccc acaccctcct tggccagttc 1020 ttccagggct ggggcacctg ggtggcttcg tggcctctga ccatcctggt gctgtctgtc 1080 atcccggtgg tggtcttggc agcgggcctg gtctttacag aactcactac ggaccccgtg 1140 gagctgtggt cggcccccaa cagccaagcc cggagtgaga aggcttttca tgaccagcat 1200 ttcggcccct tcttccgaac caaccaggtg atcctgacgg ctcctaaccg gtccagctac 1260 aggtatgact ccctgctgct ggggcccaag aacttcagcg ggatcctgga cctggacttg 1320 ctgctggagc tgctggagtt gcaggagagg ctgcggcacc tccaggtgtg gtcgcccgaa 1380 gcacagcgca acatctccct gcagcacatc tgctacgccc ccctcaatcc ggacaatacc 1440 agtctttccg attgctgcat caacagcctc ctgcagtatt tccagaacaa ccgcacgctc 1500 ctgttgctca cggccaacca gacactgatg gggcagacct cccaagtcga ctggagggac 1560 cattttctgt actgtgccaa tgccccgctc accttcaagg atggcacagc cctggccctg 1620 agctgcatgg ctgactatgg ggcccctgtc ttccccttcc ttgccgttgg ggggtacaaa 1680 gggaaggact attctgaggc ggaggccctg atcatgacgt tctccctcaa caattaccct 1740 gccggggacc cccggctggc ccaggcccag ctgtgggagg aggccttctt ggaggaaatg 1800 cgagccttcc agcgtcggac ggctggcaag ttccaggtca cgttcatggc tgagcgctct 1860 ctggaagatg agatcaatcg caccacagcc gaagacctgc ccatctttgc caccagctac 1920 attgtcatct tcctgtacat ctccctggcc ctgggcagct attccagctg gagccgagtg 1980 atggtggact ccaaggccac gctgggcctt ggcggggtgg ccgtggtcct gggagcagtc 2040 atggctgcca tgggcttctt ctcctacctg ggtatccgct cctccctgat catcctgcaa 2100 gtggtgcctt tcctggtgct gtctgtgggg gctgataaca tcttcatctt tgttctcgag 2160 taccagaggc tgccccggag gcctggggag ccgcgagagg ttcacattgg ccgagccctg 2220 ggcagggtgg cccccagcat gctgttgtgc agcctctctg aggccatctg cttcttccta 2280 ggggccctga cccccatgcc agctgtgcgg acctttgccc tgacctctgg ccttgcagtg 2340 gtccttgact tcctcctgca gatgtctgcc tttgtggccc tgctctccct ggacagcaag 2400 aggcaggagg cctcccgatt ggacgtctgc tgctgcgtca agccccggga gctgcccctg 2460 cctggccagg gagaggggtt cctgcttggc ctcttccgaa aggcctatgt ccccttcctg 2520 ctgcactgga tcactcgagg ggttgtgctg ctgctgtttc tcgccctgtt tggagtgagc 2580 ctctactaca tgtgccacat cagtgttgga ctggaccagg agctggccct gcccaaggac 2640 tcgtacctgc ttgactattt cctctttctg aaccgctact tcgagacggg ggccccggtg 2700 tactttgtta ctacctcagg ctacaacttc tccagtgagg ctgggatgaa tgccatctgc 2760 tccagtgcag gctgcaacaa cttctccttc acccagaaga tccagtatgc cacagagttc 2820 cctgagcagt cttaccttgc catccctgcc tcctcctggg tggatgactt cattgactgg 2880 ctgaccccat cctcctgctg ccgcctttat atatctggcc ccaataagga ccagttctgc 2940 ccctcgactg tcaactccct gaactgccta aagaactgcc tgagcatcac gatgggctct 3000 gtgaggccct cagtggagca gttctataag tatcttccct ggttcctgaa tgaccggccc 3060 aacatcaaat gtcccaaagg cggcctggga gcatacagca cctctgtgaa cttgacttca 3120 gatggccagg ttttagcctc caggttcatg gcctatcaca agcccctgaa aaactcacag 3180 gattacacag aagctctgcg ggcagctcgg gagctggcag ccaacatcac tgctgacctg 3240 cggaaggtgc ctgggacaga cccagctttt gaggtcttcc cctacacggt caccaatgtg 3300 ttttatgagc agtacctgac cattctccct gaggggctct tcatgctcag cctctgcctg 3360 gtgcccacct tcgctgtctg ctgcctcctg ctgggcctgg acctgcgctc cggcctcctc 3420 aacctgctgt ccatcatcat gatcctcgtg gacaccgttg gcttcatggc cctgtggggc 3480 atcagttaca atgctgtgtc cctcatcaac ctggtctcgg cggtgggcat gtctgtggag 3540 ttcgtgtccc acattacccg ctcctttgcc atcagcacca agcccacccg gctggagagg 3600 gccaaagagg ccaccatctc tatgggaagt gcggtgtttg caggtgtggc catgaccaac 3660 ctccctggca tcctggtcct gggccttgcc aaggcccagc tcattcagat cttcttcttc 3720 cgcctcaacc tcctgattac tctgctgggt ctgctgcatg gcttggtctt cctgcctgtc 3780 atcctcagct atgtggggcc tgacatcaac ccagctctgg cactggagca gaagctggct 3840 gaggaggcag cagcggcagc catagcggcc tcctacccaa atcacccctc ccgagtctcc 3900 acagctgaca acatctatgt caaccacagc tttgaaggtt ctatcaaagg tgctggtgcc 3960 gtcagcaact tcttgcccaa caatgggcgg cagttctga 3999 (SEQ ID NO: 8)    1 MAEAGLRGWL LWALLLHLAQ SEPYTPIHQP GYCAFYDECG KNPELSGGLM   51 TLSNVSCLSN TPARNITGDH LILLQRICPR LYTGPNTQAC CSAKQLVSLE  101 ASLSITKALL TRCPACSDNF VSLNCHNTCS PNQSLFINVT RVAQLGAGQL  151 PAVVAYEAFY QHSFAEQSYD SCSRVHIPAA ATLAVGSMCG VYGSALCNAQ  201 RWLNFQGDTG NGLAPLDITF HLLEPGQAVG SGIQPLNEGV ARCNESQGDD  251 AVACSCQDCA ASCPAIAHPQ ALDSTFRLGR MPGGLVLIII LCSVFTVVAI  301 LLVGLRVAPT RDKSKTVDPK KGTSLSDKLS FSTHTLLGQF FQGWGTWVAS  351 WPLTILVLSV IPVVVLAAGL VFTELTTDPV ELWSAPNSQA RSEKAFHDQH  401 FGPFFRTNQV ILTAPNRSSY RYDSLLLGPK NFSGILDLDL LLELLELQER  451 LRHLQVWSPE AQRNISLQHI CYAPLNPDNT SLSDCCINSL LQYFQNNRTL  501 LLLTANQTLM GQTSQVDWRD HFLYCANAPL TFKDGTALAL SCMADYGAPV  551 FPFLAVGGYK GKDYSEAEAL IMTFSLNNYP AGDPRLAQAQ LWEEAFLEEM  601 RAFQRRTAGK FQVTFMAERS LEDEINRTTA EDLPIFATSY IVIFLYISLA  651 LGSYSSWSRV MVDSKATLGL GGVAVVLGAV MAAMGFFSYL GIRSSLIILQ  701 VVPFLVLSVG ADNIFIFVLE YQRLPRRPGE PREVHIGRAL GRVAPSMLLC  751 SLSEAICFFL GALTPMPAVR TFALTSGLAV VLDFLLQMSA FVALLSLDSK  801 RQEASRLDVC CCVKPRELPL PGQGEGFLLG LFRKAYVPFL LHWITRGVVL  851 LLFLALFGVS LYYMCHISVG LDQELALPKD SYLLDYFLFL NRYFETGAPV  901 YFVTTSGYNF SSEAGMNAIC SSAGCNNFSF TQKIQYATEF PEQSYLAIPA  951 SSWVDDFIDW LTPSSCCRLY ISGPNKDQFC PSTVNSLNCL KNCLSITMGS 1001 VRPSVEQFYK YLPWFLNDRP NIKCPKGGLG AYSTSVNLTS DGQVLASRFM 1051 AYHKPLKNSQ DYTEALRAAR ELAANITADL RKVPGTDPAF EVFPYTVTNV 1101 FYEQYLTILP EGLFMLSLCL VPTFAVCCLL LGLDLRSGLL NLLSIIMILV 1151 DTVGFMALWG ISYNAVSLIN LVSAVGMSVE FVSHITRSFA ISTKPTRLER 1201 AKEATISMGS AVFAGVAMTN LPGILVLGLA KAQLIQIFFF RLNLLITLLG 1251 LLHGLVFLPV ILSYVGPDIN PALALEQKLA EEAAAAAIAA SYPNHPSRVS 1301 TADNIYVNHS FEGSIKGAGA VSNFLPNNGR QF* Cynomolgus Monkey NPC1L1 ORF (SEQ ID NO: 9) atggcggagg ccggcctgag gggctggctg ctgtgggccc tgctcctgca cttggcccag 60 agcgagcctt acacacccat ccaccagcct ggctactgcg ccttctatga cgaatgtggg 120 aagaacccag agctgtctgg aggcctcatg acactctcca acgtgtcctg tctgtccaac 180 acgccagccc gcaacatcac aggtgatcac ctgatcctat tacagaggat ctgcccccgc 240 ctctacaccg gccccaacac ccaagcctgc tgctccgcca agcagctggt atcattggaa 300 gcgagtctgt cgatcaccaa ggccctcctc acccgctgcc cagcctgctc tgacaatttc 360 gtgagcctgc actgccacaa cacatgcagc cccaaccaga gcctcttcat caatgtgacc 420 cgcgtggctc agctaggggc tggacaactc ccagctgtgg tggcctatga ggccttctac 480 cagcacagct ttgccgagca gagctatgac tcctgcagcc gtgtgcacat ccctgcggct 540 gccacgctgg ctgtgggcag catgtgtggc gtgtatggct ctgccctttg caatgcccag 600 cgctggctca acttccaggg agacacaggc aatggtctgg ccccactgga catcaccttc 660 cacctcttgg agcccggcca ggctgtgggg agtgggattc agcctctgaa tgagggggtt 720 gcacgttgca atgagtccca aggtgacgac gcagtggcct gctcctgcca ggactgtgct 780 gcatcctgtc ctgccatcgc ccatccccag gccctggact ccaccttccg cctgggccgg 840 atgccgggtg ggctggtcct catcatcatc ctctgttctg tcttcactgt ggtcgccatc 900 ctgctcgtgg gactccgtgt ggcccccacc agggacaaaa gcaagacggt ggaccccaag 960 aagggcacca gcctctctga caagctcagc ttctccaccc acaccctcct tggccagttc 1020 ttccagggct ggggcacctg ggtggcttcg tggcctctga ccatcctggt gctgtctgtc 1080 atcccggtgg tggtcttggc agcgggcctg gtctttacag aactcactac agaccccgtg 1140 gagctgtggt cggcccccaa cagccaagcc cggagtgaga aggcttttca tgaccagcat 1200 ttcggcccct tcttccgaac caaccaggtg atcctgacgg ctcctaaccg gtccagctac 1260 aggtatgact ccctgctgct ggggcccaag aacttcagcg ggatcctgga cctggacttg 1320 ctgctggagc tgctggagtt gcaggagagg ctgcggcacc tccaggtgtg gtcgcccgaa 1380 gcacagcgca acatctccct gcagcacatc tgctacgccc ccctcaatcc ggacaatacc 1440 agtctctccg attgctgcat caacagcctc ctgcagtatt tccagaacaa ccgcacgctc 1500 ctgttgctca cggccaacca gacactgatg gggcagacct cccaagtcga ctggagggac 1560 cattttctgt actgtgccaa tgccccgctc accttcaagg atggcacagc cctggccctg 1620 agctgcatgg ctgactatgg ggcccctgtc ttccccttcc ttgccgttgg ggggtacaaa 1680 gggaaggact attctgaggc ggaggccctg atcatgacgt tctccctcaa caattaccct 1740 gccggggacc cccggctggc ccaggcccag ctgtgggagg aggccttctt ggaggaaatg 1800 cgagccttcc agcgtcggac ggctggcaag ttccaggtca cgttcatggc tgagcgctct 1860 ctggaagatg agatcaatcg caccacagcc gaagacctgc ccatctttgc caccagctac 1920 attgtcatct tcctgtacat ctccctggcc ctgggcagct attccagctg gagcagagtg 1980 atggtggact ccaaggccac gctgggcctt ggcggggtgg ccgtggtcct gggagcagtc 2040 atggctgcca tgggcttctt ctcctacctg ggtatccgct cctccctgat catcctgcaa 2100 gtggtgcctt tcctggtgct gtctgtgggg gctgataaca tcttcatctt tgttctcgag 2160 taccagaggc tgccccggag gcctggggag ccgcgagagg ttcacattgg ccgagccctg 2220 ggcagggtgg cccccagcat gctgttgtgc agcctctctg aggccatctg cttcttccta 2280 ggggccctga cccccatgcc agctgtgcgg acctttgccc tgacctctgg ccttgcagtg 2340 gtccttgact tcctcctgca gatgtctgcc tttgtggccc tgctctccct ggacagcaag 2400 aggcaggagg cctcccgatt ggacgtctgc tgctgcgtca agccccggga gctgcccctg 2460 cctggccagg gagaggggtt cctgcttggc ctcttccgaa aggcctatgt ccccttcctg 2520 ctgcactgga tcactcgagg ggttgtgctg ctgctgtttc tcgccctgtt tggagtgagc 2580 ctctactaca tgtgccacat cagtgttgga ctggaccagg agctggccct gcccaaggac 2640 tcgtacctgc ttgactattt cctctttctg aaccgctact tcgagacggg ggccccggtg 2700 tactttgtta ctacctcagg ctacaacttc tccagtgagg ctgggatgaa tgccatctgc 2760 tccagtgcag gctgcaacaa cttctccttc acccagaaga tccagtatgc cacagagttc 2820 cctgagcagt cttaccttgc catccctgcc tcctcctggg tggatgactt cattgactgg 2880 ctgaccccat cctcctgctg ccgcctttat atatctggcc ccaataagga ccagttctgc 2940 ccctcgactg tcaactccct gaactgccta aagaactgcc tgagcatcac gatgggctct 3000 gtgaggccct cagtggagca gttctataag tatcttccct ggttcctgaa tgaccggccc 3060 aacatcaaat gtcccaaagg cggcctggga gcatacagca cctctgtgaa cttgacttca 3120 gatggccagg ttttagcctc caggttcatg gcctatcaca agcccctgaa aaactcacag 3180 gattacacag aagctctgcg ggcagctcgg gagctggcag ccaacatcac tgctgacctg 3240 cggaaggtgc ctgggacaga cccagctttt gaggtcttcc cctacacggt caccaatgtg 3300 ttttatgagc agtacctgac cattctccct gaggggctct tcatgctcag cctctgcctg 3360 gtgcccacct tcgctgtctg ctgcctcctg ctgggcctgg acctgcgctc cggcctcctc 3420 aacctgctgt ccatcatcat gatcctcgtg gacaccgttg gcttcatggc cctgtggggc 3480 atcagttaca atgctgtgtc cctcatcaac ctggtctcgg cggtgggcat gtctgtggag 3540 ttcgtgtccc acattacccg ctcctttgcc atcagcacca agcccacccg gctggagagg 3600 gccaaagagg ccaccatctc tatgggaagt gcggtgtttg caggtgtggc catgaccaac 3660 ctccctggca tcctggtcct gggccttgcc aaggcccagc tcattcagat cttcttcttc 3720 cgcctcaacc tcctgattac tctgctgggt ctgctgcatg gcttggtctt cctgcctgtc 3780 atcctcagct atgtggggcc tgacatcaac ccagctctgg cactggagca gaagctggct 3840 gaggaggcag cagcggcagc catagcggcc tcctacccaa atcacccctc ccgagtctcc 3900 acagctgaca acatctatgt caaccacagc tttgaaggtt ctatcaaagg tgctggtgcc 3960 gtcagcaact tcttgcccaa caatgggcgg cagttctga 3999 (SEQ ID NO: 10)    1 MAEAGLRGWL LWALLLHLAQ SEPYTPIHQP GYCAFYDECG KNPELSGGLM   51 TLSNVSCLSN TPARNITGDH LILLQRICPR LYTGPNTQAC CSAKQLVSLE  101 ASLSITKALL TRCPACSDNF VSLHCHNTCS PNQSLFINVT RVAQLGAGQL  151 PAVVAYEAFY QHSFAEQSYD SCSRVHIPAA ATLAVGSMCG VYGSALCNAQ  201 RWLNFQGDTG NGLAPLDITF HLLEPGQAVG SGIQPLNEGV ARCNESQGDD  251 AVACSCQDCA ASCPAIAHPQ ALDSTFRLGR MPGGLVLIII LCSVFTVVAI  301 LLVGLRVAPT RDKSKTVDPK KGTSLSDKLS FSTHTLLGQF FQGWGTWVAS  351 WPLTILVLSV IPVVVLAAGL VFTELTTDPV ELWSAPNSQA RSEKAFHDQH  401 FGPFFRTNQV ILTAPNRSSY RYDSLLLGPK NFSGILDLDL LLELLELQER  451 LRHLQVWSPE AQRNISLQHI CYAPLNPDNT SLSDCCINSL LQYFQNNRTL  501 LLLTANQTLM GQTSQVDWRD HFLYCANAPL TFKDGTALAL SCMADYGAPV  551 FPFLAVGGYK GKDYSEAEAL IMTFSLNNYP AGDPRLAQAQ LWEEAFLEEM  601 RAFQRRTAGK FQVTFMAERS LEDEINRTTA EDLPIFATSY IVIFLYISLA  651 LGSYSSWSRV MVDSKATLGL GGVAVVLGAV MAAMGFFSYL GIRSSLIILQ  701 VVPFLVLSVG ADNIFIFVLE YQRLPRRPGE PREVHIGRAL GRVAPSMLLC  751 SLSEAICFFL GALTPMPAVR TFALTSGLAV VLDFLLQMSA FVALLSLDSK  801 RQEASRLDVC CCVKPRELPL PGQGEGFLLG LFRKAYVPFL LHWITRGVVL  851 LLFLALFGVS LYYMCHISVG LDQELALPKD SYLLDYFLFL NRYFETGAPV  901 YFVTTSGYNF SSEAGMNAIC SSAGCNNFSF TQKIQYATEF PEQSYLAIPA  951 SSWVDDFIDW LTPSSCCRLY ISGPNKDQFC PSTVNSLNCL KNCLSITMGS 1001 VRPSVEQFYK YLPWFLNDRP NIKCPKGGLG AYSTSVNLTS DGQVLASRFM 1051 AYHKPLKNSQ DYTEALRAAR ELAANITADL RKVPGTDPAF EVFPYTVTNV 1101 FYEQYLTILP EGLFMLSLCL VPTFAVCCLL LGLDLRSGLL NLLSIIMILV 1151 DTVGFMALWG ISYNAVSLIN LVSAVGMSVE FVSHITRSFA ISTKPTRLER 1201 AKEATISMGS AVFAGVAMTN LPGILVLGLA KAQLIQIFFF RLNLLITLLG 1251 LLHGLVFLPV ILSYVGPDIN PALALEQKLA EEAAAAAIAA SYPNHPSRVS 1301 TADNIYVNHS FEGSIKGAGA VSNFLPNNGR QF*

Screening Assays

The invention allows the discovery of selective agonists and antagonists of NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8, or 10) that may be useful in treatment, prevention and management of a variety of medical conditions including elevated serum sterol (e.g., cholesterol) or 5α-stanol. Thus, NPC1L1 of this invention can be employed in screening systems to identify agonists or antagonists. For example, the screening assays of the present invention, comprising use of canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1, can be used to identify an agonist or antagonist of NPC1L1 from the same or a different organism (e.g., an antagonist of human NPC1L1). In an embodiment of the invention, these systems provide methods for bringing together NPC1L1, an appropriate, known ligand or agonist or antagonist (e.g., compound 1, 2, 3, 4, 5, 6, 7, 8 or 9), including a sterol (e.g., cholesterol, phytosterols (including, but not limited to, sitosterol, campesterol, stigmasterol and avenosterol)), a cholesterol oxidation product, a 5α-stanol (including but not limited to cholestanol, 5α-campestanol and 5α-sitostanol), a substituted azetidinone (e.g., ezetimibe), BODIPY-ezetimibe (Altmann, et al., (2002) Biochim. Biophys. Acta 1580(1):77-93) or 4″, 6″-bis[(2-fluorophenyl)carbamoyl]-beta-D-cellobiosyl derivative of 11-ketotigogenin as described in DeNinno, et al., (1997) (J. Med. Chem. 40(16):2547-54) (Merck; L-166,143) or any substituted azetidinone, and a sample to be tested for the presence of an NPC1L1 agonist or antagonist.

A convenient method by which to evaluate whether a sample contains an NPC1L1 agonist or antagonist is to determine whether the sample contains a substance which competes for binding between the known agonist or antagonist (e.g., ezetimibe) and NPC1L1.

In an embodiment of the invention, an antagonist of an NPC1L1 of the invention (e.g., canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8, or 10)) is used to treat, prevent or manage hypercholesterolemia (e.g., primary hypercholesterolemia, homozygous familial hypercholesterolemia (HoFH)), sitosterolemia (e.g., homozygous sitosterolemia), hyperlipidemia, hypertriglyceridemia, arteriosclerosis, atherosclerosis or hypertension. In an embodiment of the invention, an NPC1L1 antagonist is used to treat, prevent or manage any of the foregoing disorders in human or non-human animals (e.g., dogs, cats, rabbits, hamsters, monkeys, rats, mice, cows). For example, a veterinary hyperlipidemic disorder such as primary idiopathic hyperlipidemia can be treated with an NPC1L1 antagonist. Primary idiopathic hyperlipidemia has been reported in a variety of canine breeds including miniature Schnauzers, beagles, mixed breeds, poodles, shelties as well as in cats. Dogs with diabetes mellitus, hypothyroidism, Cushings disease, liver Disease and nephrotic Syndrome have been reported with hyperlipidemia. Hypercholesterolemia (which may also be treated, prevented or managed with an NPC1L1 antagonist) has also been reported in dogs such as Shetland sheepdogs and has been observed in dogs with canine hypothyroidism.

The term “specific” when used to describe binding of, for example, a ligand or antagonist of NPC1L1 in a screening assay is a term of art which refers to the extent by which the ligand or antagonist (e.g., detectably labeled substituted azetidinone, detectably labeled ezetimibe, detectably labeled sterol (e.g., cholesterol) or detectably labeled 5α-stanol, e.g., [³H]-glucuronidated ezetimibe or BODIPY-labeled ezetimibe) binds preferentially to NPC1L1 over that of other proteins in the assay system. For example, an antagonist or ligand of NPC1L1 binds specifically to NPC1L1 when the signal generated in the assay to indicate such binding exceeds, to any extent, a background signal in a negative control experiment wherein, for example, NPC1L1 or the known antagonist or ligand is absent. Furthermore, “specific binding” includes binding of an antagonist or ligand either directly to NPC1L1 or indirectly, for example via another moiety, in a complex of which NPC1L1 is a part. The moiety to which an NPC1L1 ligand or antagonist binds can be another protein or a post-translational modification of NPC1L1 (e.g., a lipid chain or a carbohydrate chain).

Non-limiting examples of suitable azetidinones include those disclosed in U.S. Pat. Nos. RE37,721; 5,631,365; 5,767,115; 5,846,966; 5,688,990; 5,656,624; 5,624,920; 5,698,548 and 5,756,470 and U.S. Patent Application Publication No 2003/0105028, each of which is herein incorporated by reference in its entirety.

Ezetimibe can be prepared by a variety of methods well know to those skilled in the art, for example such as are disclosed in U.S. Pat. Nos. 5,631,365, 5,767,115, 5,846,966, 6,207,822, U.S. Patent Application Publication No. 2002/0193607 and PCT Patent Application WO 93/02048, each of which is incorporated herein by reference in its entirety.

“Sample”, “candidate compound” or “candidate substance” refers to a composition which is evaluated in a test or assay, for example, for the ability to agonize or antagonize NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8, or 10) or a functional fragment thereof. The composition may be a small organic or inorganic molecule, peptide, nucleotide, polynucleotide, subatomic particle (e.g., α particles, β particles) or antibody or fragment thereof.

NPC1L1 for use in an assay of the invention (e.g., any set forth below) can be from any suitable source. For example, a nucleic acid encoding an NPC1L1 polypeptide of the invention (e.g., SEQ ID NO: 1, 3, 5, 7, or 9) can be transfected into an appropriate host cell (e.g., HEK293), whereby the receptor will become incorporated into the membrane of the cell. A membrane fraction can then be isolated from the cell and used as a source of the receptor for assay. Alternatively, the whole cell expressing the receptor on the cell surface can be used in an assay. In an embodiment, free NPC1L1 is used or a highly soluble fragment of NPC1L1 is generated and used in an assay of the invention.

Two basic types of screening systems that can be used include, a labeled-ligand binding assay (e.g., direct binding assay or scintillation proximity assay (SPA)) and a “sterol (e.g., cholesterol) or 5α-stanol uptake” assay. A labeled ligand, for use in the binding assay, can be obtained by labeling a sterol (e.g., cholesterol) or a 5α-stanol or a known NPC1L1 agonist or antagonist with a measurable group (e.g., ¹²⁵I or ³H). Various labeled forms of sterols (e.g., cholesterol) or 5α-stanols are available commercially or can be generated using standard techniques (e.g., Cholesterol-[1,2-³H(N)], Cholesterol-[1,2,6,7-³H(N)] or Cholesterol-[7-³H(N)]; American Radiolabeled Chemicals, Inc; St. Louis, Mo.). In an embodiment of the invention, ezetimibe is fluorescently labeled with a BODIPY group (Altmann, et al., Biochim. Biophys. Acta 1580(1):77-93 (2002)) or labeled with a detectable group such as ¹²⁵I or ³H.

Direct Binding Assay. Typically, a given amount of NPC1L1 of the invention (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) or an active fragment thereof is contacted with increasing amounts of labeled ligand or known antagonist or agonist (discussed above) and the amount of the bound, labeled ligand or known antagonist or agonist is measured after removing unbound, labeled ligand or known antagonist or agonist by washing. As the amount of the labeled ligand or known agonist or antagonist is increased, a point is eventually reached at which all receptor binding sites are occupied or saturated. Specific receptor binding of the labeled ligand or known agonist or antagonist is abolished by a large excess of unlabeled ligand or known agonist or antagonist.

In an embodiment of the invention, an assay system is used in which non-specific binding of the labeled ligand or known antagonist or agonist to the receptor is minimal. Non-specific binding is typically less than 50%, preferably less than 15%, and more preferably less than 10% of the total binding of the labeled ligand or known antagonist or agonist. Preferably, specific binding of the labeled ligand or known antagonist or agonist to an untransfected/untransformed host cell or to a membrane fraction from an untransfected/untransformed host cell will be negligible.

In the basic binding assay, the method for identifying an NPC1L1 agonist or antagonist includes:

-   -   (a) contacting canine, rabbit, hamster, rhesus monkey or         cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) or         a subsequence thereof, in the presence of a known amount of         detectably labeled sterol (e.g., cholesterol) or 5α-stanol or         known antagonist or agonist (e.g., [³H]-glucuronidated ezetimibe         or BODIPY-labeled ezetimibe) with a sample to be tested for the         presence of an NPC1L1 agonist or antagonist; and     -   (b) measuring the amount of labeled sterol (e.g., cholesterol)         or 5α-stanol or known antagonist or agonist bound to NPC1L1.

An NPC1L1 antagonist or agonist in the sample is identified by measuring substantially reduced binding of the labeled sterol (e.g., cholesterol) or 5α-stanol or known antagonist or agonist to NPC1L1, compared to what would be measured in the absence of such an antagonist or agonist. For example, reduced binding between [³H]-cholesterol and NPC1L1 in the presence of a sample would indicate that the sample contains a substance which is competing against [³H]-cholesterol for NPC1L1 binding.

In an embodiment of the invention, this assay includes a negative-control experiment lacking any NPC1L1-dependent ligand (e.g., [³H]-glucuronidated ezetimibe or BODIPY-labeled ezetimibe) binding. In an embodiment of the invention, for example, a whole cell or cell membrane lacking any functional NPC1L1, e.g., untransformed HEK293, is assayed for ligand binding. When screening a sample for the presence of an NPC1L1 antagonist, it is useful to compare the level of binding observed in the presence of a sample being tested with that of a control experiment, as described herein, which completely lacks NPC1L1-dependent binding. Ideally, though by no means necessarily, the level of binding seen in the presence of a sample containing an antagonist will be similar to that of the negative-control experiment. If no significant binding is observed, then this indicates that the assay is operating properly.

In another embodiment of the invention, a positive-control experiment is performed in conjunction with the assay. In this embodiment, for example, NPC1L1 is bound to a detectably labeled substance which is known to bind (e.g. ³H-ezetimibe) and, then, exposed to a blank. If binding is observed (e.g., where the labeled substance is competed off of the NPC1L1 by the unlabeled substance), then this indicates that the assay is working properly.

Alternatively, a sample can be tested directly for binding to canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10). In an embodiment of the invention, a basic assay of this type includes the following steps:

(a) contacting canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10), a subsequence thereof with a detectable or detectably labeled candidate substance (e.g., small molecule or an antibody); and

(b) detecting direct binding between the candidate substance and NPC1L1.

Again, these experiment can be performed along with a negative-control experiment wherein NPC1L1-dependent binding is completely lacking. For example, the assay can be performed using a whole cell or cell membrane lacking any functional NPC1L1 (e.g., untransformed HEK293 cells) and/or lacking any candidate substance. If no binding is observed, then this indicates that the assay is working properly.

In an embodiment of the invention, a positive-control assay is performed. In such an assay, a detectable or detectably labeled substance known to bind to NPC1L1 (e.g., ³H-labeled compound 4) is assayed for binding. If binding is observed, then this indicates that the assay is operating properly.

The scope of the present invention includes a method for assaying candidate inhibitory agents for activity against cholesterol absorption (e.g., intestinal cholesterol absorption, for example, in the intestine of a human) comprising the steps of: providing a cell expressing canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) or a functional fragment or variant thereof which is capable of binding a fluorescent cholesterol absorption inhibitor, e.g., wherein said inhibitor is an azetidinone; contacting said cell with a candidate inhibitory agent in the presence of said fluorescent cholesterol absorption inhibitor; and measuring the inhibition of the fluorescence of said cell, wherein a relative absence of fluorescent cholesterol absorption inhibitor indicates that said candidate inhibitory agent is an inhibitory agent which inhibits cholesterol absorption into the cell (e.g., intestinal cholesterol absorption). In an embodiment of the invention, the fluorescent cholesterol absorption inhibitor is

wherein R comprises a fluorescent moiety, e.g., whereing the fluorescent moiety linked by an alkynyl-containing tether group (e.g., C1, C2, C3, C4, C5, C6, C7, C8, C9 or C10 alkynyl group). In an embodiment of the invention, R is

The scope of the present invention includes a method for identifying inhibitory agents which inhibit the absorption of cholesterol into or onto a cell membrane or which inhibit cholesterol absorption e.g., in the intestine of a human, said method comprising the steps of: (a) combining a fluorescent cholesterol absorption inhibitor e.g., wherein said inhibitor is an azetidinone, said cell membrane, wherein the cell membrane comprises canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) or a functional fragment or variant thereof on its surface or embedded within the membrane in such a manner that the NPC1L1 is capable of mediating cholesterol transport across the membrane or binding or transport of a cholesterol absorption inhibitor, and a candidate inhibitory agent, under conditions wherein, but for the presence of said inhibitory agent, said fluorescent cholesterol absorption inhibitor is bound to the membrane e.g., by the NPC1L1; and (b) detecting the relative presence or absence of fluorescent cholesterol absorption inhibitor bound to the membrane, wherein a relative absence of fluorescent cholesterol absorption inhibitor indicates that said candidate inhibitory agent is an inhibitory agent which inhibits cholesterol absorption into or onto the membrane or which inhibits cholesterol absorption into the intestine. In an embodiment of the invention, the cell membrane is an intestinal epithelial cell membrane. In an embodiment of the invention, the fluorescent cholesterol absorption inhibitor is

wherein R comprises a fluorescent moiety, e.g., whereing the fluorescent moiety linked by an alkynyl-containing tether group. In an embodiment of the invention, R is

The presence of fluorescent inhibitor in the cell or bound to the membrane in these methods would indicate that the candidate inhibitory agent is not an inhibitor of cholesterol absorption.

The present invention also includes any azetidinone, such as ezetimibe or any fluorescent cholesterol absorption inhibitor (e.g., a fluorescently labeled azetidinone) bound to canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) or a functional fragment or variant thereof (e.g., isolated NPC1L1 e.g., soluble or on the surface of an isolated cell or membrane or non-isolated, in vivo NPC1L1, for example, on the surface of a cell), e.g., wherein the inhibitor is

wherein R comprises a fluorescent moiety, e.g., whereing the fluorescent moiety linked by an alkynyl-containing tether group. In an embodiment of the invention, R is

U.S. Pat. Nos. 7,144,696; 6,933,107; 6,632,933; and 6,593,078 are herein incorporated by reference in their entireties as is published international application no. WO 00/63703.

A candidate compound which is found to bind to NPC1L1 may function as an agonist or antagonist of NPC1L1 (e.g., by inhibition of sterol (e.g., cholesterol) or 5α-stanol uptake). This may be confirmed, subsequently, in an uptake assay as discussed below.

SPA Assay. NPC1L1 antagonists or agonists may also be measured using scintillation proximity assays (SPA). SPA assays are conventional and very well known in the art; see, for example, U.S. Pat. No. 4,568,649. In SPA, the target of interest is immobilised to a small microsphere approximately 5 microns in diameter. The microsphere, typically, includes a solid scintillant core which has been coated with a polyhydroxy film, which in turn contains coupling molecules, which allow generic links for assay design. When a radioisotopically labeled molecule binds to the microsphere, the radioisotope is brought into close proximity to the scintillant and effective energy transfer from electrons emitted by the isotope will take place resulting in the emission of light. While the radioisotope remains in free solution, it is too distant from the scintillant and the electron will dissipate the energy into the aqueous medium and therefore remain undetected. Scintillation may be detected with a scintillation counter. In general, ³H and ¹²⁵I labels are well suited to SPA.

For the assay of receptor-mediated binding events, the lectin wheat germ agglutinin (WGA) may be used as the SPA bead coupling molecule (Amersham Biosciences; Piscataway, N.J.). The WGA coupled bead captures glycosylated, cellular membranes and glycoproteins and has been used for a wide variety of receptor sources and cultured cell membranes. The receptor is immobilized onto the WGA-SPA bead and a signal is generated on binding of an isotopically labeled ligand. Other coupling molecules which may be useful for receptor binding SPA assays include poly-L-lysine and WGA/polyethyleneimine (Amersham Biosciences; Piscataway, N.J.). See, for example, Berry, J. A., et al., (1991) Cardiovascular Pharmacol. 17 (Suppl. 7): S143-S145; Hoffman, R., et al., (1992) Anal. Biochem. 203: 70-75; Kienhus, et al., (1992) J. Receptor Research 12: 389-399; Jing, S., et al., (1992) Neuron 9: 1067-1079.

The scintillant contained in SPA beads may include, for example, yttrium silicate (YSi), yttrium oxide (YOx), diphenyloxazole or polyvinyltoluene (PVT) which acts as a solid solvent for diphenylanthracine (DPA).

SPA assays may be used to analyze whether a sample contains an NPC1L1 antagonist or agonist. In these assays, canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 or a host cell which expresses canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) on the cell surface or a membrane fraction thereof is incubated with and captured by SPA beads (e.g., WGA coated YOx beads or WGA coated YSi beads). The beads bearing the NPC1L1 are incubated with labeled, known ligand or agonist or antagonist (e.g., ³H-labeled compound 4). The assay mixture further includes either the sample to be tested or a blank (e.g., water). After an optional incubation, scintillation is measured using a scintillation counter. An NPC1L1 agonist or antagonist may be identified in the sample by measuring substantially reduced fluorescence, compared to what would be measured in the absence of such agonist or antagonist (blank). Measuring substantially reduced fluorescence suggests that the sample contains a substance which competes for NPC1L1 binding with the known ligand, agonist or antagonist.

In an embodiment of the invention, a negative-control assay is performed. In a negative-control assay, for example, the assay is performed as set forth above except that no NPC1L1 is present. If no significant fluorescence is observed, then this indicates that the assay is operating properly.

In an embodiment of the invention, a positive-control assay is performed. In a positive-control assay, the substance known to bind to NPC1L1 (e.g., ³H-labeled compound 4) is incubated along with an un-radiolabeled substance also known to bind to NPC1L1 (e.g., unlabeled compound 4). If reduced binding of the labeled substance is observed (i.e., reduced fluorescence), relative to an assay wherein a blank is used in place on the unlabeled substance known to bind NPC1L1, then this indicates that the assay is operating properly.

Alternatively, a sample may be identified as an antagonist or agonist of NPC1L1 by directly detecting binding in a SPA assay. In this assay, a labeled version of a candidate compound to be tested is put in contact with canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 or a host cell expressing NPC1L1 or a membrane fraction thereof which is bound to the SPA bead. Fluorescence may then be assayed to detect the presence of a complex between the labeled candidate compound and the NPC1L1. A candidate compound which binds to NPC1L1 may possess NPC1L1 agonistic or antagonistic activity.

SPA Assays can also be performed along with a negative-control experiment lacking any NPC1L1-dependent binding. The control experiment can be performed, for example, with a cell or cell membrane lacking any functional NPC1L1. When the control experiment is performed, the level of binding observed in the presence of sample being tested for the presence of an antagonist can be compared with that observed in the control experiment. If no significant binding is observed, this indicates that the assay is operating properly.

Furthermore, a positive-control experiment can be performed wherein a radiolabeled compound known to bind to NPC1L1 (e.g., ³H-labeled compound 4) is assayed. If binding is observed, this indicates that the assay is operating properly.

Host cells expressing NPC1L1 may be prepared by transforming or transfecting a nucleic acid encoding an NPC1L1 of the invention into an appropriate host cell, whereby the receptor becomes incorporated into the membrane of the cell. A membrane fraction can then be isolated from the cell and used as a source of the receptor for assay. Alternatively, the whole cell expressing the receptor on the cell surface can be used in an assay. Preferably, specific binding of the labeled ligand or known antagonist or agonist to an untransfected/untransformed host cell or membrane fraction from an untransfected/untransformed host cell will be negligible. Preferred host cells include Chinese Hamster Ovary (CHO) cells, murine macrophage J774 cells or any other macrophage cell line and human intestinal epithelial Caco2 cells.

Sterol/5α-stanol Uptake Assay. Assays may also be performed to determine if a sample can agonize or antagonize NPC1L1 mediated sterol (e.g., cholesterol) or 5α-stanol uptake. In these assays, a host cell expressing canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8 or 10) on the cell surface (discussed above) is contacted with detectably labeled sterol (e.g., ³H-cholesterol or ¹²⁵I-cholesterol)) or 5α-stanol along with a sample to be tested for an agonist or antagonist of NPC1L1. After an optional incubation, the cells can be washed to remove unabsorbed sterol or 5α-stanol. Sterol or 5α-stanol uptake can be determined by detecting the presence of labeled sterol or 5α-stanol in the host cells. For example, assayed cells or lysates or fractions thereof (e.g., fractions resolved by thin-layer chromatography) can be contacted with a liquid scintillant and scintillation can be measured using a scintillation counter.

In these assays, an NPC1L1 antagonist in the sample may be identified by measuring substantially reduced uptake of the labeled sterol (e.g., ³H-cholesterol) or 5α-stanol, compared to what would be measured in the absence of such an antagonist and an agonist may be identified by measuring substantially increased uptake of the labeled sterol (e.g., ³H-cholesterol) or 5α-stanol, compared to what would be measured in the absence of such an agonist.

Uptake assays can optionally be performed along with a negative-control assay lacking any NPC1L1-dependent uptake. The negative-control assay can be performed, for example, with a cell lacking any functional NPC1L1 (e.g., an untransformed host cell) or lacking any labeled sterol or 5α-stanol. A substantial lack of uptake indicates that the assay is operating correctly. A positive-control assay may also be optionally performed along with an assay of the invention. For example, in a control assay, a cell expressing NPC1L1 is exposed to labeled sterol or 5α-stanol in the absence of any antagonist. A high level of uptake in the cell would indicate that the assay is operating correctly.

In Vivo Assay. The present invention comprises a mutant, transgenic canine, rabbit, hamster, rhesus monkey or cynomolgus monkey which lacks any functional NPC1L1. This canine, rabbit, hamster, rhesus monkey or cynomolgus monkey may serve as a convenient control experiment in screening assays for identifying inhibitors of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption, preferably inhibitors of NPC1L1. In an embodiment of the invention, a canine, rabbit, hamster, rhesus monkey or cynomolgus monkey-based assay of the present invention would comprise the following steps:

-   -   (a) feeding a sterol (e.g., cholesterol) or 5α-stanol-containing         substance (e.g., comprising radiolabeled cholesterol, such as         ¹⁴C-cholesterol or ³H-cholesterol) to a first and second canine,         rabbit, hamster, rhesus monkey or cynomolgus monkey comprising a         functional NPC1L1 gene and to a third, mutant canine, rabbit,         hamster, rhesus monkey or cynomolgus monkey lacking a functional         NPC1L1;

In an embodiment of the invention, the sterol (e.g., cholesterol) or 5α-stanol containing substance contains labeled cholesterol, such as a radiolabeled cholesterol, for example, ³H or ¹⁴C labeled cholesterol. The sterol (e.g., cholesterol) or 5α-stanol containing substance may also include cold, unlabeled sterol (e.g., cholesterol) or 5α-stanol such as in corn oil.

In these assays, the third npc1l1 mutant canine, rabbit, hamster, rhesus monkey or cynomolgus monkey serves as a (+)-control experiment which exhibits low levels of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption and the second canine, rabbit, hamster, rhesus monkey or cynomolgus monkey serves as a (−)-control experiment which exhibits normal, uninhibited levels of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption. The second canine, rabbit, hamster, rhesus monkey or cynomolgus monkey is not administered the sample to be tested for an NPC1L1 antagonist. The first canine, rabbit, hamster, rhesus monkey or cynomolgus monkey is the experimental.

-   -   (b) administering the sample to be tested for the presence of         the antagonist to the first canine, rabbit, hamster, rhesus         monkey or cynomolgus monkey comprising a functional NPC1L1 but         not to the second canine, rabbit, hamster, rhesus monkey or         cynomolgus monkey;     -   (c) measuring the amount of sterol (e.g., cholesterol) or         5α-stanol absorption in the intestine of said first, second and         third canine, rabbit, hamster, rhesus monkey or cynomolgus         monkey;

Intestinal sterol (e.g., cholesterol) or 5α-stanol absorption may be measured by any method known in the art. For example, the level intestinal absorption can be assayed by measuring the level of serum sterol (e.g., cholesterol) or 5α-stanol.

-   -   (d) comparing the levels of intestinal sterol (e.g.,         cholesterol) or 5α-stanol absorption in each canine, rabbit,         hamster, rhesus monkey or cynomolgus monkey;         wherein the sample is determined to contain the intestinal         sterol (e.g., cholesterol) or 5α-stanol absorption antagonist         when the level of intestinal sterol (e.g., cholesterol) or         5α-stanol absorption in the first canine, rabbit, hamster,         rhesus monkey or cynomolgus monkey and in the third canine,         rabbit, hamster, rhesus monkey or cynomolgus monkey are less         than the amount of intestinal sterol (e.g., cholesterol) or         5α-stanol absorption in the second canine, rabbit, hamster,         rhesus monkey or cynomolgus monkey.

Preferably, if the sample contains an intestinal sterol (e.g., cholesterol) or 5α-stanol absorption inhibitor (e.g., an NPC1L1 inhibitor), the level of sterol (e.g., cholesterol) or 5α-stanol absorption in the first canine, rabbit, hamster, rhesus monkey or cynomolgus monkey will be similar to that of the third, npc1l1 mutant canine, rabbit, hamster, rhesus monkey or cynomolgus monkey.

An alternative positive-control experiment which may be used in conjunction with these screening assays is to perform the experiment essentially as set forth above, except that the sample tested is ezetimibe. If inhibition of uptake is observed in this assay, this indicates that the assay is operating properly.

Antibodies

The present invention includes any antibody or antigen-binding fragment thereof that binds specifically to canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 or an antigenic fragment thereof. Embodiments of the invention include any anti-canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antibody or antigen-binding fragment thereof which is a monoclonal antibody, polyclonal antibody, bispecific antibody, linear antibody, chimeric antibody, humanized antibody, anti-idiotypic antibody, recombinant antibody, Fab antibody fragment, F(ab)₂ antibody fragment, Fv antibody fragment (e.g., VH or VL), single chain Fv antibody fragment or dsFv antibody fragment.

The present invention also includes any antibody or antigen-binding fragment thereof which binds specifically to canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 or an antigenic fragment thereof which was raised against said NPC1L1 or fragment thereof. For example, an embodiment of the invention includes any anti-canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antibody or antigen-binding fragment thereof produced by immunization of an animal with said NPC1L1 or an antigenic fragment thereof.

In an embodiment of the invention, a polyclonal antibody is raised in animals by multiple subcutaneous (sc) or intraperitoneal (ip) injections of the relevant antigen (e.g., canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 or an antigenic fragment thereof) and an adjuvant. It may be useful to conjugate the relevant antigen to a protein that is immunogenic in the species to be immunized, e.g., keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, or soybean trypsin inhibitor using a bifunctional or derivatizing agent, for example, maleimidobenzoyl sulfosuccinimide ester (conjugation through cysteine residues), N-hydroxysuccinimide (through lysine residues), glutaraldehyde, succinic anhydride, SOCl₂, or R1N═C═NR, where R and R1 are different alkyl groups. In an embodiment of the invention, animals are immunized against the antigen, immunogenic conjugates, or derivatives by combining, e.g., 100 μg or 5 μg of the protein or conjugate (for rabbits or mice, respectively) with 3 volumes of Freund's complete adjuvant and injecting the solution intradermally at multiple sites. One month later the animals are boosted with ⅕ to 1/10 the original amount of peptide or conjugate in Freund's complete adjuvant by subcutaneous injection at multiple sites. Seven to 14 days later the animals are bled and the serum is assayed for antibody titer. Animals are boosted until the titer plateaus. In an embodiment of the invention, the animal is boosted with the conjugate of the same antigen, but conjugated to a different protein and/or through a different cross-linking reagent. Conjugates also can be made in recombinant cell culture as protein fusions. Also, aggregating agents such as alum are suitably used to enhance the immune response.

In an embodiment of the invention, a monoclonal antibody is made using the hybridoma method first described by Kohler et al., Nature, 256:495 (1975), or by recombinant DNA methods (see e.g., U.S. Pat. No. 4,816,567). In an embodiment of the invention, in the hybridoma method, a mouse or other appropriate host animal, such as a hamster or macaque monkey, is immunized as hereinabove described to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the protein used for immunization. Alternatively, lymphocytes may be immunized in vitro. Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986)). In an embodiment of the invention, the hybridoma cells thus prepared are seeded and grown in a suitable culture medium that, in an embodiment of the invention, contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells. For example, if the parental myeloma cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells. In an embodiment of the invention, myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. Among these, myeloma cell lines are murine myeloma lines. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987)).

In an embodiment of the invention, culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against the antigen. In an embodiment of the invention, the binding specificity of monoclonal antibodies produced by hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). In an embodiment of the invention, after hybridoma cells are identified that produce antibodies of the desired specificity, affinity, and/or activity, the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986)). Suitable culture media for this purpose include, for example, D-MEM or RPMI-1640 medium. In addition, the hybridoma cells may be grown in vivo as ascites tumors in an animal. In an embodiment of the invention, the monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography. In an embodiment of the invention, DNA encoding the monoclonal antibodies is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the monoclonal antibodies). The hybridoma cells serve as a source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.

In an embodiment of the invention, antibodies or antibody fragments of the invention can be isolated from antibody phage libraries generated using the techniques described in McCafferty et al., Nature, 348:552-554 (1990). Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991) describe the isolation of murine and human antibodies, respectively, using phage libraries. Subsequent publications describe the production of high affinity (nM range) human antibodies by chain shuffling (Marks et al., Bio/Technology, 10:779-783 (1992)), as well as combinatorial infection and in vivo recombination as a strategy for constructing very large phage libraries (Waterhouse et al., Nuc. Acids. Res., 21:2265-2266 (1993)). Thus, these techniques are viable alternatives to traditional monoclonal antibody hybridoma techniques for isolation of monoclonal antibodies.

In an embodiment of the invention, single-chain Fv or sFv antibody fragments comprise the VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain. Generally, the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the sFv to form the desired structure for antigen binding. For a review of sFv see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds. Springer-Verlag, New York, pp. 269-315 (1994).

In an embodiment of the invention, humanized antibody forms of non-human (e.g., murine) antibodies are chimeric antibodies which contain minimal sequence derived from non-human immunoglobulin. In general, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region (e.g., CDRs) of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity. In some instances, Fv framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.

A linear antibody is an antibody fragment as described in Zapata et al. Protein Eng. 8(10):1057-1062 (1995). Briefly, these fragments comprise a pair of tandem Fd segments (VH—CH1-VH—CH1) which form a pair of antigen binding regions. Linear antibodies can be bispecific or monospecific.

A species-dependent antibody is one which has a stronger binding affinity for an antigen from a first species than it has for a homologue of that antigen from a second species. In an embodiment of the invention, a species-dependent antibody “binds specifically” to a canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antigen (e.g., has a binding affinity (Kd) value of no more than about 1×10⁻⁷ M) but has a binding affinity for a homologue of the antigen from a second species (e.g., another mammalian species such as human NPC1L1) which is at least about 50 fold, or at least about 500 fold, or at least about 1000 fold, weaker than its binding affinity for the canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antigen. The present invention comprises species dependent anti-canine, rabbit, hamster, cynomolgus monkey and rhesus monkey NPC1L1 antibodies and antigen-binding fragments thereof.

The present invention also includes an anti-canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antibody or antigen-binding fragment thereof produced by a process including introduction of an expression vector comprising the light and/or heavy chain of said antibody into a suitable host cell, expressing said chain(s) in said cell and, optionally isolating said chain(s). For example, an embodiment of the invention includes expressing an anti-canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antibody or antigen-binding fragment thereof of the invention in the plasmid system set forth in published international application no. WO2005/047512.

The present invention also includes any immunoliposome including any anti-canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1 antibody or antigen-binding fragment thereof of the invention. An immunoliposome is a liposome including said antibody or fragment. Liposomes containing the antibody or fragment can be prepared by methods known in the art, such as described in Epstein et al., Proc. Natl. Acad. Sci. USA, 82:3688 (1985); Hwang et al., Proc. Natl. Acad. Sci. USA, 77:4030 (1980); and U.S. Pat. Nos. 4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Pat. No. 5,013,556. Other useful liposomes can be generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter. Fab fragments of an antibody of the present invention can be conjugated to the liposomes as described in Martin et al. J. Biol. Chem. 257: 286-288 (1982) via a disulfide interchange reaction. In an embodiment, a chemotherapeutic agent (such as ezetimibe) is optionally contained within the liposome.

In an embodiment of the invention, an anti-canine NPC1L1 antibody, an anti-hamster NPC1L1 antibody, an anti-rabbit NPC1L1 antibody, an anti-rhesus monkey NPC1L1 antibody or an anti-cynomolgus monkey NPC1L1 antibody that “specifically binds” to or is “specific for” canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1, respectively, is one that binds to that particular polypeptide or an epitope on the polypeptide without substantially binding to any other polypeptide or epitope.

In an embodiment of the invention, an anti-canine NPC1L1 antibody, an anti-hamster NPC1L1 antibody, an anti-rabbit NPC1L1 antibody, an anti-rhesus monkey NPC1L1 antibody or an anti-cynomolgus monkey NPC1L1 antibody that “specifically binds” to or is “specific for” canine, hamster, rabbit, rhesus monkey or cynomolgus monkey NPC1L1, respectively, is one that binds to that particular polypeptide or an epitope on the polypeptide with an affinity constant of at least 10⁻⁶ M, or at least 10⁻⁸ M.

If necessary, non-specific binding can be reduced without substantially affecting specific binding by varying the binding conditions. The appropriate binding conditions such as concentration of antibodies, ionic strength of the solution, temperature, time allowed for binding, concentration of a blocking agent (e.g., serum albumin, milk casein), etc., may be optimized by a skilled artisan using routine techniques

The present invention further comprises a complex comprising an antibody (e.g., an isolated antibody) or antigen-binding fragment thereof of the present invention (e.g., an anti-canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 antibody) bound to a polypeptide of the present invention (e.g., canine, rabbit, hamster, rhesus monkey or cynomolgus monkey NPC1L1 (e.g., SEQ ID NO: 2, 4, 6, 8, or 10) or any fragment thereof (e.g., an antigenic fragment)). In an embodiment of the invention, the polypeptide is isolated. The present invention includes complexes existing both in vitro as well as in vivo (e.g., in the body of a subject). For example, the present invention includes a complex comprising an isolated antibody of the invention, that was administered to a subject, existing in a complex with an NPC1L1 polypeptide of the present invention, in the body of said subject. Furthermore, the present invention includes a complex comprising a non-isolated antibody, bound to an isolated NPC1L1 polypeptide of the present invention that was administered to a subject (e.g., for the purpose of generating anti-NPC1L1 antibodies), inside or outside the body of said subject.

Pharmaceutical Compositions

NPC1L1 agonists and antagonists discovered, for example, by the screening methods described above may be used therapeutically (e.g., in a pharmaceutical composition) to stimulate or block the activity of NPC1L1 and, thereby, to treat any medical condition caused or mediated by NPC1L1. In addition, the antibodies and antigen-binding fragments thereof of the invention may also be used therapeutically (e.g., in a pharmaceutical composition) to bind NPC1L1 and, thereby, block the ability of NPC1L1 to bind a sterol (e.g., cholesterol) or 5α-stanol. Blocking the binding of a sterol (e.g., cholesterol) or 5α-stanol to NPC1L1 prevents absorption of the molecule (e.g., by intestinal cells such as enterocytes). Blocking absorption of sterol (e.g., cholesterol) or 5α-stanol is a useful way to lower serum sterol (e.g., cholesterol) or 5α-stanol levels in a subject and, thereby, reduce the incidence of, for example, hyperlipidemia, atherosclerosis, coronary heart disease, stroke or arteriosclerosis.

The term “subject” or “patient” includes any organism, preferably animals, more preferably mammals such as humans, hamsters, rhesus monkeys, cynomolgus monkeys, mice, rats, rabbits, dogs, canines, horses, primates, cats).

The term “pharmaceutical composition” refers to a composition including an active ingredient and a pharmaceutically acceptable carrier and/or adjuvant.

Although the compositions of this invention could be administered in simple solution, they may be used in combination with other materials such as carriers, preferably pharmaceutically acceptable carriers. Useful, pharmaceutically acceptable carriers can be any compatible, non-toxic substances suitable for delivering the compositions of the invention to a subject. Sterile water, alcohol, fats, waxes, and inert solids may be included in a pharmaceutically acceptable carrier. Buffering agents or dispersing agents may also be incorporated into the pharmaceutical composition.

In an embodiment of the invention, the pharmaceutical compositions of the invention are in the form of a pill or capsule. Methods for formulating pills and capsules are very well known in the art. For example, for oral administration in the form of tablets or capsules, the active drug component may be combined with any oral, non-toxic pharmaceutically acceptable inert carrier, such as lactose, starch, sucrose, cellulose, magnesium stearate, dicalcium phosphate, calcium sulfate, talc, mannitol, ethyl alcohol (liquid forms) and the like. Moreover, when desired or needed, suitable binders, lubricants, disintegrating agents and coloring agents may also be incorporated in the mixture. Suitable binders include, for example, starch, gelatin, natural sugars, corn sweeteners, natural and synthetic gums such as acacia, sodium alginate, carboxymethylcellulose, polyethylene glycol and waxes. Among the lubricants that may be used in a pharmaceutical composition are boric acid, sodium benzoate, sodium acetate, sodium chloride, and the like. Disintegrants include starch, methylcellulose, guar gum and the like. Sweetening and flavoring agents and preservatives may also be included where appropriate.

The pharmaceutical compositions of the invention may be administered in association with a second pharmaceutical composition or substance. In an embodiment of the invention, the second composition includes a cholesterol-lowering drug (e.g., simvastatin, atorvastatin, lovastatin, pravastatin, rosuvastatin or fluvastatin). The term “in association with” indicates that the components of the combinations of the invention can be formulated into a single composition for simultaneous delivery or formulated separately into two or more compositions (e.g., a kit). Furthermore, each component of a combination of the invention can be administered to a subject at a different time than when the other component is administered; for example, each administration may be given non-simultaneously (e.g., separately or sequentially) at several intervals over a given period of time. Moreover, the separate components may be administered to a subject by the same or by a different route (e.g., orally, intravenously, subcutaneously).

The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. See, e.g., Gilman et al. (eds.) (1990), The Pharmacological Bases of Therapeutics, 8th Ed., Pergamon Press; and Remington's Pharmaceutical Sciences, supra, Easton, Pa.; Avis et al. (eds.) (1993) Pharmaceutical Dosage Forms: Parenteral Medications Dekker, New York; Lieberman et al. (eds.) (1990) Pharmaceutical Dosage Forms: Tablets Dekker, New York; and Lieberman et al. (eds.) (1990), Pharmaceutical Dosage Forms: Disperse Systems Dekker, New York.

The dosage regimen involved in a therapeutic application may be determined by a physician, considering various factors which may modify the action of the therapeutic substance, e.g., the condition, body weight, sex and diet of the patient, the severity of any infection, time of administration, and other clinical factors. Often, treatment dosages are titrated upward from a low level to optimize safety and efficacy. Dosages may be adjusted to account for the smaller molecular sizes and possibly decreased half-lives (clearance times) following administration.

An “effective amount” of an antagonist of the invention may be an amount that will detectably reduce the level of intestinal sterol (e.g., cholesterol) or 5α-stanol absorption or detectably reduce the level of serum sterol (e.g., cholesterol) or 5α-stanol in a subject administered the composition.

Typical protocols for the therapeutic administration of such substances are well known in the art. Pharmaceutical composition of the invention may be administered, for example, by any parenteral or non-parenteral route.

Pills and capsules of the invention can be administered orally. Injectable compositions can be administered with medical devices known in the art; for example, by injection with a hypodermic needle.

Injectable pharmaceutical compositions of the invention may also be administered with a needleless hypodermic injection device; such as the devices disclosed in U.S. Pat. Nos. 5,399,163; 5,383,851; 5,312,335; 5,064,413; 4,941,880; 4,790,824 or 4,596,556.

Anti-Sense

The present invention also encompasses anti-sense oligonucleotides capable of specifically hybridizing to mRNA encoding NPC1L1 (e.g., any of SEQ ID NOs: 1, 3, 5, 7, or 9) having an amino acid sequence defined by, for example, SEQ ID NO: 2, 4, 6, 8, or 10 or a subsequence thereof so as to prevent translation of the mRNA. Additionally, this invention contemplates anti-sense oligonucleotides capable of specifically hybridizing to the genomic DNA molecule encoding NPC1L1.

This invention further provides pharmaceutical compositions comprising (a) an amount of an oligonucleotide effective to reduce NPC1L1-mediated sterol (e.g., cholesterol) or 5α-stanol absorption by passing through a cell membrane and binding specifically with mRNA encoding NPC1L1 in the cell so as to prevent its translation and (b) a pharmaceutically acceptable carrier capable of passing through a cell membrane. In an embodiment, the oligonucleotide is coupled to a substance that inactivates mRNA. In another embodiment, the substance that inactivates mRNA is a ribozyme.

Reducing the level of NPC1L1 expression by introducing anti-sense NPC1L1 RNA into the cells of a patient is a useful method reducing intestinal sterol (e.g., cholesterol) or 5α-stanol absorption and serum cholesterol in the patient.

Kits

Kits of the present invention include ezetimibe, e.g., combined with a pharmaceutically acceptable carrier, in a pharmaceutical formulation, e.g., in a pharmaceutical dosage form such as a pill, a powder, an injectable liquid, a tablet, dispersible granules, a capsule, a cachet or a suppository. See for example, Gilman et al. (eds.) (1990), The Pharmacological Bases of Therapeutics, 8th Ed., Pergamon Press; and Remington's Pharmaceutical Sciences, supra, Easton, Pa.; Avis et al. (eds.) (1993) Pharmaceutical Dosage Forms: Parenteral Medications Dekker, New York; Lieberman et al. (eds.) (1990) Pharmaceutical Dosage Forms: Tablets Dekker, New York; and Lieberman et al. (eds.) (1990), Pharmaceutical Dosage Forms: Disperse Systems Dekker, New York. In an embodiment of the invention, the dosage form is a Zetia® (ezetimibe) or Vytorin® (ezetimibe/simvastatin) tablet (Merck/Schering-Plough Corp.).

The kits of the present invention also include information, for example in the form of a package insert, indicating that the target of ezetimibe is NPC1L1. The term “target of ezetimibe” indicates that ezetimibe reduces intestinal sterol (e.g., cholesterol) or 5α-stanol absorption, either directly or indirectly, by antagonizing NPC1L1. The form of the insert may take any form, such as paper or on electronic media such as a magnetically recorded medium (e.g., floppy disk) or a CD-ROM.

The package insert may also include other information concerning the pharmaceutical compositions and dosage forms in the kit. Generally, such information aids patients and physicians in using the enclosed pharmaceutical compositions and dosage forms effectively and safely. For example, the following information may be supplied in the insert: pharmacokinetics, pharmacodynamics, clinical studies, efficacy parameters, indications and usage, contraindications, warnings, precautions, adverse reactions, overdosage, proper dosage and administration, how supplied, proper storage conditions, references and patent information.

The kits of the invention may also include simvastatin (

combined, in an embodiment of the invention, with a pharmaceutically acceptable carrier, in a pharmaceutical formulation, more preferably in a pharmaceutical dosage form such as a pill, a powder, an injectable liquid, a tablet, dispersible granules, a capsule, a cachet or a suppository. In an embodiment of the invention, the dosage form of simvastatin is a Zocor® tablet (Merck & Co.; Whitehouse Station, N.J.).

Ezetimibe and simvastatin may be supplied, in the kit, as separate compositions or combined into a single composition. For example, ezetimibe and simvastatin may be supplied within a single, common pharmaceutical dosage form (e.g., pill or tablet) or in separate pharmaceutical dosage forms (e.g., two separate pills or tablets).

npc1l1⁻ Cells

The present invention provides any isolated canine, rabbit, hamster, rhesus monkey or cynomolgus monkey cell which lacks an NPC1L1 gene which encodes or can produce a functional NPC1L1 protein. Included within this embodiment are mutant npc1l1 genes comprising a point mutation, truncation or deletion of the genetic coding region (partly or in its entirety) or of any regulatory element (e.g., a promoter).

For example, the cell can be isolated from a mutant animal comprising a homozygous or heterozygous mutation of endogenous, chromosomal NPC1L1 wherein the animal does not produce any functional NPC1L1 protein. Moreover, the present invention comprises any cell, tissue, organ, fluid, nucleic acid, peptide or other biological substance derived or isolated from such an animal. The isolated cell can be isolated or derived, for example, from the duodenum, gall bladder, liver, small intestine or stomach of the mutant animal. Further, the cell can be an enterocyte.

The npc1l1⁻ mutant cells are useful, for example, for use in control experiments in screening assays (see e.g., supra) since they lack any NPC1L1-dependent uptake or binding of sterol, 5α-stanol or ezetimibe. The level of inhibition caused by a particular sample, in a screening assay, can be compared to that of an assay performed with the mutant cell. Ideally, though by no means necessarily, in a screening assay, for example, as described herein, the same amount of binding will be observed by a non-mutant cell or cell membrane, in the presence of an antagonist, as is observed in connection with a mutant npc1l1⁻ cell or cell membrane alone.

Transgenic Animals

Genetically engineered host cells can be further used to produce non-human transgenic animals such as canines (e.g., dogs), rabbits, hamsters, cynomolgus monkeys and rhesus monkeys. A transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal in one or more cell types or tissues of the transgenic animal. These animals are useful for studying the function of NPC1L1 and identifying and evaluating modulators (e.g., inhibitors) thereof. The present invention includes for example, knock-out canines (e.g., dogs), rabbits, hamsters, cynomolgus monkeys and rhesus monkeys which lack any functional NPC1L1 protein in their cells. The present invention also includes any transgenic non-human animal comprising a supra-normal level of an NPC1L1 of the invention in its cells.

A transgenic animal can be produced by introducing nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection or retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal. Any of the NPC1L1 nucleotide sequences of the invention can be introduced as a transgene into the genome of an animal.

Any of the regulatory or other sequences useful in expression vectors can form part of the transgenic sequence. This includes intronic sequences and polyadenylation signals, if not already included. A tissue-specific regulatory sequence(s) can be operably linked to the transgene to direct expression of NPC1L1 protein to particular cells.

Methods for generating transgenic animals via embryo manipulation and microinjection have become conventional in the art and are described. Any technique known in the art may be used to introduce the transgene (i.e., nucleic acids of the invention) into animals to produce the founder lines of transgenic animals. Such techniques include, but are not limited to, pronuclear microinjection (Paterson et al., Appl. Microbiol. Biotechnol. 40:691-698 (1994); Carver et al., Biotechnology (NY) 11:1263-1270 (1993); Wright et al., Biotechnology (NY) 9:830-834 (1991); and Hoppe et al., U.S. Pat. No. 4,873,191 (1989)); retrovirus mediated gene transfer into germ lines (Van der Putten et al., Proc. Natl. Acad. Sci., USA 82:6148-6152 (1985)), blastocysts or embryos; gene targeting in embryonic stem cells (Thompson et al., Cell 56:313-321 (1989)); electroporation of cells or embryos (Lo, Mol Cell. Biol. 3:1803-1814 (1983)); introduction of the polynucleotides of the invention using a gene gun (see, e.g., Ulmer et al., Science 259:1745 (1993); introducing nucleic acid constructs into embryonic pleuripotent stem cells and transferring the stem cells back into the blastocyst; and sperm-mediated gene transfer (Lavitrano et al., Cell 57:717-723 (1989); etc. For a review of such techniques, see Gordon, “Transgenic Animals,” Intl. Rev. Cytol. 115:171-229 (1989), which is incorporated by reference herein in its entirety. See also Gordon, “Transgenic Animals,” Intl. Rev. Cytol. 115:171-229 (1989); U.S. Pat. No. 5,464,764 (Capecchi, et al., Positive-Negative Selection Methods and Vectors); U.S. Pat. No. 5,631,153 (Capecchi, et al., Cells and Non-Human Organisms Containing Predetermined Genomic Modifications and Positive-Negative Selection Methods and Vectors for Making Same); U.S. Pat. No. 4,736,866 (Leder, et al., Transgenic Non-Human Animals); and U.S. Pat. No. 4,873,191 (Wagner, et al., Genetic Transformation of Zygotes). As stated, any technique known in the art may be used to produce transgenic clones containing polynucleotides of the invention, for example, nuclear transfer into enucleated oocytes of nuclei from cultured embryonic, fetal, or adult cells induced to quiescence (Campell et al., Nature 380:64-66 (1996); Wilmut et al., Nature 385:810-813 (1997)).

In one embodiment of the invention, a transgenic canine (e.g., dog), hamster, rabbit, cynomolgus monkey or rhesus monkey is a “knock-out” animal having a heterozygous or homozygous alteration in the sequence of an endogenous NPC1L1 gene that results in a decrease of NPC1L1 function, e.g., such that NPC1L1 expression is undetectable or insignificant. Knock-out animals are typically generated by homologous recombination with a vector comprising a transgene having at least a portion of the gene to be knocked out. A deletion, addition or substitution can be introduced into the transgene to functionally disrupt it. Detailed methodologies for homologous recombination in transgenic animals are available (see Capecchi, Science (1989) 244:1288-1292; Joyner et al., Nature (1989) 338:153-156). Other procedures for the production of transgenic animals are also available (Pursel et al., Science (1989) 244:1281-1288; Simms et al., Bio/Technology (1988) 6:179-183).

A transgenic founder animal can be identified based upon the presence of the transgene in its genome and/or expression of transgenic mRNA in tissues or cells of the animals. For example, once transgenic animals have been generated, the expression of the recombinant gene may be assayed utilizing standard techniques. Initial screening may be accomplished by Southern blot analysis or PCR techniques to analyze animal tissues to verify that integration of the transgene has taken place. The level of mRNA expression of the transgene in the tissues of the transgenic animals may also be assessed using techniques which include, but are not limited to, Northern blot analysis of tissue samples obtained from the animal, in situ hybridization analysis, and reverse transcriptase-PCR (rt-PCR). Samples of transgenic gene-expressing tissue may also be evaluated immunocytochemically or immunohistochemically using antibodies specific for the transgene product. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene can further be bred to other transgenic animals carrying other transgenes.

Any cell, tissue, gamete, organ, fluid, nucleic acid, peptide or other biological substance derived or isolated from a transgenic animal of the invention is within the scope of the present invention as is any offspring of such an animal (e.g., any offspring inheriting the transgene).

EXAMPLES

The invention is further illustrated by the following non-limiting example.

Example 1 Binding and Inhibition of NPC1L1 Orthologues by Ezetimibe and Related Compounds

This example demonstrates that the NPC1L1 genes set forth herein bind to ezetimibe and structurally related compounds.

Materials and Methods

Materials. The [³H]-ezetimibe glucuronide (EZE-gluc) [1-([2, 6-3H]-4-fluorophenyl)-(3R)-[3-(4-fluorophenyl)-(3S)-hydroxypropyl]-(4S)-[3,5-³H]-4-hydroxyphenyl)-2-azetidinone; 34.5 Ci/mmol (Garcia-Calvo et al., Proc. Natl. Acad. Sci. U.S.A. 102:8132-8137 (2005)) and several 2-azetidinone based compounds.

cDNA cloning. Cloning and sequencing of NPC1L1 from human (Genbank AY437865), rat (Genbank AY437867) and mouse (Genbank AY437865) have been reported (Altmann et al., Science 303:1201-1204 (2004) and U.S. published patent application nos. US2004/0093629; US 2004/0137467; US 2004/0132058 and US 2004/0161838). Jejunal enterocytes were isolated as previously described (Altmann et al., Biochim. Biophys. Acta 1580:77-93 (2002)) from freshly isolated tissue samples from rhesus monkey, cynomolgus monkey, hamster, rabbit and beagle dog. Isolated enterocytes were immediately extracted with Tri-reagent and the total RNA isolated following manufacturer's instructions (Molecular Research Center Inc.; Cincinnati, Ohio). Messenger RNA was isolated using FastTrack 2.0 (Invitrogen; Carlsbad, Calif.) and cDNA prepared using superscript Choice System (Life Technologies; Gaithersburg, Md.) following oligo-(dT) primed first strand synthesis. NPC1L1 specific oligo primers corresponding to highly conserved regions in the human, mouse and rat were used in varied combinations to polymerase chain reaction (PCR) amplify each cDNA sample. PCR products were sequenced to determine species specific NPC1L1 sequence. To obtain species-specific gene sequences from the 5′-start codon region and the 3′-stop codon region, 5′- and 3′ RACE PCR were performed using Marathon-Ready cDNA Amplification Kit, or Smart RACE cDNA Amplification Kit according to the manufacturer's instructions (BD Biosciences Clontech; Mountain View, Calif.). The species-specific oligonucleotide primers for 5′ and 3′ RACE PCR were designed according to available species-specific NPC1L1 gene sequences. In some cases, oligo primers based upon consensus gene sequences among species were also used in the 5′ and 3′-RACE PCR reaction. Sequence analysis of RACE PCR products identified coding sequence for the start and stop of the protein open reading frame. Preparation of the final NPC1L1 cDNA was carried out by PCR amplification of the complete ORF using species specific forward and reverse primers encompassing the start and stop codons respectively:

Rabbit NPC1L1:

-   -   5′-end sequence was obtained by 5′-RACE PCR with primer set of         S1352 (TAGGCCCGCTCGGCGAAGCTGCGCTCG) (SEQ ID NO: 11) and primer         #98 (AGCTAGCTTGCCAAACCTACAGGT) (SEQ ID NO: 12).     -   3′-end sequence was obtained by 3′-RACE PCR with primer set of         S1299 (CATGTCTGTGGAGTTYGTGTCCCACAT) (SEQ ID NO: 13) and primer         #98 (AGCTAGC TTGCCAAACCTACAGGT) (SEQ ID NO: 12).     -   The complete ORF sequence was obtained by PCR with primer set of         S1368 (ATGGCAGGGGCTGCGCGGGGCTGGCTG) (SEQ ID NO: 14) and S1317         (TCAGAACTTC TGCTTTCTGGTGGG) (SEQ ID NO: 15)         Rhesus Monkey NPC1L1     -   5′-end sequence was obtained by 5′-RACE PCR with primer S1320R         (TARAAGGCCTCATAGGCCACCAC) (SEQ ID NO: 16).     -   3′-end sequence was obtained by 3′-RACE PCR with primer set of         S1299 (CATGTCTGTGGAGTTYGTGTCCCACAT) (SEQ ID NO: 13) and primer         #98 (AGCTAGC TTGCCAAACCTACAGGT) (SEQ ID NO: 12).     -   The complete ORF sequence was obtained by PCR with primer set of         monkey 5′ primer (ATGGCGGAGGCCGGCCTGAGGGGCTGGCTG) (SEQ ID         NO: 17) and Monkey 3′ primer (TCAGAA CTGCCGCCCATTGTTGGGCAAGAA)         (SEQ ID NO: 18)         Hamster NPC1L1     -   5′-end sequence was obtained by 5′-RACE PCR with 5′ hamster GSP2         primer (TGACATTGATGAAGAGGCTCTGGTCAGG) (SEQ ID NO: 19).     -   3′-end sequence was obtained by 3′-RACE PCR with 5′ hamster GSP2         primer (TCAGGCATCCTCAACCTGCTCTCCATCAT) (SEQ ID NO: 20).     -   The complete ORF sequence was obtained by PCR with primer set of         hamster 5′ primer (ATGGCAGCTGGCCTAACGAGATGGCTG) (SEQ ID NO: 21)         and hamster 3′ primer (TTAAAACTT TTGGCCGCTTTTAGGCAAG) (SEQ ID         NO: 22)         Canine NPC1L1     -   The complete ORF sequence was obtained by PCR with primer set of         S1406 (ATGGCGGACACTGGCCAGGGGCT) (SEQ ID NO: 23) and S1414         (TCAGAGGTCCGGT CCACTGCGGGG) (SEQ ID NO: 24)         Cynomologus Monkey NPC1L1     -   The complete ORF sequence was obtained by PCR with primer set of         monkey 5′ primer (ATGGCGGAGGCCGGCCTGAGGGGCTGGCTG) (SEQ ID         NO: 17) and Monkey 3′ primer (TCAGAACTGCCGCCCATTGTTGGGCAAGAA)         (SEQ ID NO: 18)

Sequencing of multiple clones from independent PCR reactions resulted in cDNA sequences free from nucleotide errors introduced by Taq polymerase.

Cell Culture and Membrane Preparation. Each plasmid pCR3.1 harboring NPC1L1 was prepared using standard molecular biology protocols. Stable cell lines expressing human, rhesus monkey, mouse, rat, hamster, canine or rabbit NPC1L1 were generated using Lipofectamine 2000 transfection reagent in HEK-293 cells according to the manufacturer's protocol. Cells were maintained in DMEM supplemented with 10% FBS, 100 U/ml pen/strep, and 500 μg/ml geneticin at 37° C., 5% CO₂. All cell culture reagents were obtained from Invitrogen Life Technologies, (Carlsbad, Calif.). Cell membranes were prepared by lysing cells in 5 mM HEPES with protease inhibitors (Complete™ Protease Inhibitor Cocktail Tablets; Roche Diagnostics Corp., Indianapolis Ind.) for 15 min at 4° C. A membrane pellet was obtained by centrifuging the cell lysates at 12,000×g for 25 min. The membranes were resuspended in 5 mM HEPES with protease inhibitors and triturated with a 21 G needle.

NPC1L1 Binding Assays

Fluorescence. Cells were plated into 384-well black/clear plates (BD Biosciences, Bedford Mass.) for binding experiments the following day. The media was aspirated. Media (20 μl) containing 250 nM BODIPY-labeled glucuronidated ezetimibe (compound 1; Burnett et al., Bioorganic and Medicinal Chemistry Letters 12:315-318 (2002)) was added to each well. Media (20 μl) containing the indicated concentration of compound was then added to the wells. Unlabeled glucuronidated ezetimibe (compound 4; 100 μM) was used to determine nonspecific binding. The binding reaction was allowed to proceed for 4 hours at 37° C. Subsequently the media was aspirated and the cells washed once with PBS. The remaining BODIPY-labeled glucuronidated ezetimibe (compound 1) bound to the cells was quantified using a FlexStation plate reader (Molecular Devices, Sunnyvale Calif.).

Radioligand. Binding of [³H]-glucuronidated ezetimibe (compound 4) to membranes from cells expressing NPC1L1 was measured using filtration (Garcia-Calvo et al., Proc. Natl. Acad. Sci. U.S.A. 102:8132-8137 (2005)). Reactions were performed in binding buffer (5 mM HEPES, 5.5 mM glucose, 117 mM NaCl and 5.4 mM KCl, pH 7.4). Cell membranes (50 μg in 20 μl) were added to each well. Subsequently, [³H]-glucuronidated ezetimibe (compound 4; 20 nM; 20 μl) was added to each well. Compounds (20 μl) were then added to the wells as indicated in the figure legends. Nonspecific binding was determined by including unlabeled glucuronidated ezetimibe (compound 4; 100 μM) in the binding reaction. Binding reactions were incubated for 2 hours at 37° C. Samples were transferred to Unifilter-96 GF/C plates (Perkin Elmer, Wellesley Mass.) and filtered using a Brandel harvester (Gaithersburg Md.). The plates were washed several times with cold wash buffer (120 mM NaCl, 0.1% Sodium Cholate, 20 mM MES pH 6.7) and dried. Liquid scintillant (50 μl; Microscint-20, Perkin Elmer, Wellesley Mass.) was added and the bound radioactivity was measured using a microplate scintillation counter.

Acute cholesterol absorption assay. ¹⁴C-cholesterol absorption was determined acutely in rats using conditions previously described (Van Heek et al., J. Pharmacol. Exp. Ther. 283: 157-163 (1997)). Compounds were dissolved in rat bile and delivered (1.0 ml) intraduodenally by bolus injection via an intestinal catheter, followed by 1.0 ml saline rinse (0.9%). Following a 30 min incubation, a cholesterol emulsion containing 3 mg cholesterol and 2 μCi ¹⁴C-cholesterol (3 ml) was delivered to each rat as a bolus via intestinal catheter, followed by 1 ml saline rinse. Animals were sacrificed 90 min later and ¹⁴C-cholesterol levels in plasma, liver, intestinal contents, and intestinal wall were determined.

Results

The effective dose of ezetimibe that inhibits cholesterol absorption varies among several species that have been studied. Since NPC1L1 has been identified as the direct proximal target of ezetimibe, we cloned NPC1L1 from jejunal enterocytes of rhesus and cynomolgus monkey, canine, hamster, and rabbit (see SEQ ID NOs: 1-10). Comparison of the amino acid sequences of NPC1L1 in those species along with previously published amino acid sequences of human, rat, and mouse NPC1L1 (Altmann et al., Science 303:1201-1204 (2004)) and predicted sequences from chimpanzee (Genbank XM_(—)519072) and cow (Genbank XM_(—)588051) are shown in FIG. 7. At the sequence level, the positions of the Cys residues, of which there are ˜40, are highly conserved across all species and suggestive of a highly constrained structure. Several Cys residues are located within predicted transmembrane helices 1, 6 and 9 with the potential of fixing these transmembrane helices in close proximity. The proposed protein topology defined by the predicted transmembrane helices is consistent with the location of the putative N-linked glycosylation sites which reside in three large extracellular loops exposed to the intestinal lumen. FIG. 1 presents a ball model of the predicted membrane topology of human NPC1L1 (Iyer et al., Biochim. Biophys. Acta 1722:382-392 (2005)). Residues in black constitute the sterol sensing domain (SSD) (Carstea et al., Science 277:228-231 (1997)) and residues shaded gray identify non-conserved positions between human and monkey NPC1L1. NPC1L1 is most highly conserved among the primates with human, chimpanzee and monkey exhibiting >95% amino acid identity (FIG. 2A). Nucleotide sequences in rhesus and cynomolgus monkey coding regions show only 9 substitutions, none of which result in amino acid differences (data not shown). Human and monkey NPC1L1 amino acid sequences are highly homologous being less than 5% divergent. Of the 53 amino acid substitutions in monkey, 28 reside in the extracellular domain and 17 are located within the cytoplasmic domains. The remaining 8 changes occur in the transmembrane domains, 2 of which are located in the SSD.

The rodent family, consisting of sequences from hamster, rat, and mouse, also exhibit strong homology to each other with close to 90% identity in amino acid sequences. Primates and rodents share only 77-78% amino acid sequence identity with each other. The homology of canine NPC1L1 compared to the other species is relatively low (74-81%) as is cow (75-81%). Rabbit NPC1L1 also exhibits relatively low homology to the other species examined (75-79%) but is most closely associated with rodents. A phylogenetic tree representing the homology of NPC1L1 in the various species is shown in FIG. 2B. As expected, canine and cow NPC1L1 are more divergent compared to both primate and rodent families.

Binding characteristics of ezetimibe (compound 3) and its glucuronidated metabolite (compound 4) to the NPC1L1 orthologs of several species were examined herein. Stable HEK-293 cell lines expressing human, rhesus monkey, canine, rat, mouse, hamster, rabbit, or mouse NPC1L1 cDNA were derived and used in subsequent experiments. The saturation binding curves of a fluorescently-labeled (BODIPY) ezetimibe glucuronide (compound 1) to each species NPC1L1 ortholog (except mouse) are shown in FIG. 3. The calculated Kd values were: monkey 46 nM; hamster 49 nM, canine 52 nM; rat 58 nM; human 61 nM, rabbit 151 nM. Fluorescently-labeled (BODIPY) ezetimibe glucuronide (compound 1) binding to mouse NPC1L1 could not be detected despite demonstrable expression of mouse NPC1L1 in HEK-293 cells by western blot analysis (data not shown).

In an effort to show binding to mouse NPC1L1, several related ezetimibe analogs were examined as possible alternatives to fluorescently-labeled (BODIPY) ezetimibe glucuronide (compound 1) in the binding assay. Compound 2, which is a fluorescently labeled synthetic precursor for fluorescently-labeled (BODIPY) ezetimibe glucuronide (compound 1; Burnett et al., Bioorganic and Medicinal Chemistry Letters 12:315-318 (2002)), was identified as a viable option for detection of mouse NPC1L1 binding. Compound 2 contains a methyl ester substitution for the carboxylic acid on the glucuronide portion of the molecule (compound structures shown in FIG. 4A). Saturation binding analysis with compound 2 (FIG. 4B) demonstrated binding to mouse NPC1L1 with a Kd of 118 nM.

Binding affinities at each species NPC1L1 ortholog were determined for both ezetimibe (compound 3) and compound 4 (FIGS. 3 and 4C). The calculated Ki values are listed in Table 2 (columns 1 and 2) and are compared with in vivo ED50 values derived for each species tested (column 3). Divergence in the affinities of ezetimibe (compound 3) and compound 4 for NPC1L1 is consistently observed across species. For all species tested, the affinity of compound 4 for NPC1L1 is greater than that of ezetimibe (compound 3) (compare column 1 versus column 2). Against monkey NPC1L1, the difference in affinity of these two compounds is most obvious at nearly 10-fold, whereas the difference in affinity is less than 3-fold against rabbit or mouse NPC1L1. Rank order species affinity for ezetimibe (compound 3) is (monkey, dog, rat)>hamster>(human and rabbit)>>mouse. The rank order species affinity for compound 4 is slightly modified with monkey>dog>(rat and hamster)>(human and rabbit)>>mouse. By comparison, the rank order of in vivo potency of ezetimibe among species is monkey>dog>(rat and hamster)>>mouse. It should be noted that following oral administration, 90% of ezetimibe is glucuronidated thereby converting ezetimibe (compound 3) to compound 4. Therefore, the predominant form of ezetimibe present at the site of action in vivo (NPC1L1 in the jejunum) is the glucuronide compound 4. FIG. 5 shows the correlation between compound 4 or ezetimibe (compound 3) affinity and in vivo potency across multiple species. The results indicate that stronger binding to NPC1L1 by the compound produces more profound cholesterol lowering activity in vivo.

TABLE 2 Binding affinities of NPC1L1 orthologues for ezetimibe or compound 4. ezetimibe cpd. 4 ezetimibe Ki (nM) Ki (nM) ED50 (ug/kg) Human 2240 660 ND Monkey 900 92 0.5 Hamster 1530 370 40 Canine 770 192 7 Rat 970 352 30 Rabbit 2125 830 ND Mouse 5400 9000 700

Expanding the study to several other ezetimibe analogs confirms the observation that NPC1L1 binding correlates with in vivo cholesterol lowering activity. Ezetimibe analogs exhibiting in vivo cholesterol lowering activity (compound 5, compound 6 and compound 7) as well as analogs displaying no in vivo cholesterol lowering activity (compound 8 and compound 9) were evaluated for binding to NPC1L1 orthologs of multiple species. The compound structures and the Ki values at each species NPC1L1 are listed in Table 3. The in vivo data measuring inhibition of cholesterol absorption in rat (ED₅₀) and percent cholesterol lowering in plasma and liver in hamster are also provided for comparison in Table 3. The three active compounds exhibit variable affinity when evaluated against each species of NPC1L1 with the rank order of affinity among species similar to that of ezetimibe (compound 3) and compound 4. Higher affinity is observed at monkey, dog, and rat NPC1L1 and lower affinity at human and rabbit NPC1L1 with affinity for hamster NPC1L1 somewhat intermediate. In comparison, the affinities of the compounds are markedly lower at mouse NPC1L1. Compounds that lack in vivo efficacy exhibit no detectable binding to NPC1L1 orthologs from any of the species tested. These data demonstrate that compound binding to NPC1L1 translates into in vivo activity. Prediction of the extent of in vivo potency is confounded by metabolic parameters following oral administration. Glucuronidation of ezetimibe (compound 3) produces a metabolite (compound 4) with higher affinity for NPC1L1. Similar metabolism may affect related compounds. The ability to generate metabolites with high affinity for NPC1L1 will affect overall in vivo responsiveness. A determinant of in vivo efficacy is the ability of the predominant compound metabolite to bind to NPC1L1. Minor changes in compound structure or NPC1L1 amino acid sequence can affect binding affinity and consequently in vivo efficacy.

TABLE 3 Inhibition of NPC1L1 orthologues with ezetimibe and related compounds. Compound Human Monkey Mouse Hamster Rat Dog

2.24 0.9 9 1.53 0.97 0.77

0.66 0.092 5.4 0.371 0.352 0.19

2.15 0.37 7.7 1.2 0.542 1.28

4.59 1.6 16.4 2.34 1.46 1.43

3.23 3.23 21.6 4.28 2.1 2.3

Inactive Inactive Inactive Inactive Inactive Inactive

Inactive Inactive Inactive Inactive Inactive Inactive rat Compound Rabbit ED50 Liver Plasma

2.1 1.6 96 26

0.83 1.9 92 48

1.9 ND 86 36

5 ND 63 22

5.6 36 96 47

Inactive Inactive ND ND

Inactive Inactive Inactive Inactive ND = experiment not done

An example of the effects of small modifications on the binding affinity of related compounds for NPC1L1 is provided by comparison of the binding characteristics of compound 2 and compound 1 (fluorescently labeled (BODIPY) ezetimibe). The Kd of [³H]-labeled compound 4 was determined for both human and monkey NPC1L1 in saturation binding assays (FIGS. 6A & 6B). A Kd of 206 nM for human and 102 nM for monkey are consistent with previously reported values of 220 nM and 41 nM respectively (Garcia-Calvo et al., Proc. Natl. Acad. Sci. U.S.A. 102:8132-8137 (2005)). Competition binding studies using [³H]-labeled compound 4 were performed to derive Ki values for compound 1 (fluorescently labeled (BODIPY) ezetimibe) and compound 2 at both human NPC1L1 (FIG. 6C) and monkey NPC1L1 (FIG. 6D). The Ki of compound 1 (fluorescently labeled (BODIPY) ezetimibe) at human NPC1L1 is calculated to be 2.5 μM and 210 nM at monkey NPC1L1. By comparison, the Ki of compound 2 is calculated to be 120 nM and 70 nM at human and monkey NPC1L1 respectively. The results demonstrate that the small modification of substituting the methyl ester for the carboxylic acid on the glucuronide dramatically increases the affinity for human NPC1L1 (over 20-fold). In comparison, the compound modification increased affinity for monkey NPC1L1 by 3-fold. This illustrates that small variations in ezetimibe related compounds can result in markedly diverse binding interactions. Likewise, diversity in NPC1L1 may also affect the binding interaction. Although human and monkey NPC1L1 share 95% homology, the binding affinity of specific compounds varies markedly between the two species orthologs. Given the data demonstrating the correlation between NPC1L1 binding affinity and in vivo efficacy, the diversity in NPC1L1 among species may be a determinant regulating in vivo responsiveness.

Discussion

Recently, NPC1L1, an intestinally expressed protein critical to the absorption of sterols was identified as the molecular target of ezetimibe (Altmann et al., Science 303:1201-1204 (2004); Davis et al., J. Biol. Chem., 279:33586-33592 (2004), Garcia-Calvo et al., Proc. Natl. Acad. Sci. U.S.A. 102:8132-8137 (2005)). Discovery of the drug target enabled in vitro analysis of drug binding and experimental opportunities to explore the inter-species variability in ezetimibe potency and efficacy. Herein, we describe the cloning and expression of NPC1L1 in multiple species for studies comparing target interaction of ezetimibe (compound 3) and the active in vivo glucuronidated metabolite, compound 4. A novel fluorescent compound binding assay is utilized to assess the binding properties of several ezetimibe related compounds at the NPC1L1 orthologs of multiple species enabling structure activity relationships to be developed and the interaction of ezetimibe and NPC1L1 to be better understood.

Intraduodenal delivery of ezetimibe (compound 3) leads to significant levels of the compound detected in portal plasma of which >95% is the glucuronide compound 4 following first pass metabolism in the intestine. Traveling from portal plasma to the liver and back to the intestine via bile, compound 4 is redelivered to the site of action where it accumulates in the intestinal lumen (van Heek et al., Br. J. Pharmacol. 129:1748-1754 (2000)). Although both ezetimibe (compound 3) and compound 4 bind to NPC1L1, the binding affinity of compound 4 is greater than that of ezetimibe (compound 3) in all species examined consistent with the stronger potency of compound 4 observed in in vivo efficacy studies (van Heek et al., Br. J. Pharmacol. 129:1748-1754 (2000)). The compounds differ in affinity by as much as 10-fold in monkey and as little as 2-fold in mouse (Table 2), but the rank order of potency is similar for both compounds, (monkey, rat, dog, and hamster>human and rabbit>mouse) and correlates well with animal efficacy studies (Table 2). This indicates that compound potency is affected by the binding affinity of the compound for NPC1L1 of a particular species. However, the rate and efficiency of glucuronidation in each species also likely contribute to the diversity in species responsiveness to oral administration of ezetimibe given the binding differential between ezetimibe and compound 4. Indeed, compound metabolism may be a factor in determination of ezetimibe potency in species that exhibit the highest degree of separation between ezetimibe (compound 3) and compound 4 binding affinities and that are particularly responsive to ezetimibe therapy in vivo (e.g., monkey). Recently, the UDP-glucuronosyltransferase enzyme(s) responsible for glucuronidating ezetimibe (compound 3) in humans was identified (Ghosal et al., Drug. Metab. Dispos. 32: 314-320 (2004)), however little comparative information is available for this enzyme or related enzymes across multiple species.

Changes in compound structure affect NPC1L1 binding ability (Table 3). Glucuronidation of ezetimibe (compound 3) following oral administration (forming compound 4) enhances NPC1L1 binding and improves in vivo potency. By contrast, addition of a protective aromatic group to the glucuronide moiety (compound 5) causes the Ki value to revert to that observed for the nonglucuronidated form. It has previously been reported that hydroxylation of the 3-phenylpropyl side chain improves in vivo potency of this class of compounds (Burnett et al., Curr. Medicinal Chem. 11:1873-1887 (2004); Clader et al., J. Med Chem. 39:3684-3693 (1996)). Consistent with that conclusion, compounds that lack the hydroxyl group at the 3-phenylpropyl side chain exhibit decreased (compound 7) or total loss (compound 8, compound 9) of NPC1L1 binding activity.

Diversity in compounds or NPC1L1 can affect NPC1L1 binding. In FIG. 6, binding of compound 1 and compound 2 to human and monkey NPC1L1 are compared. Compound 1 is BODIPY-labeled compound 4 and differs from compound 2 only by a substitution of a methyl ester for the carboxylic acid on the glucuronide moiety (FIG. 4A) (Burnett et al., Curr. Medicinal Chem. 11:1873-1887 (2004)). Consistent with other ezetimibe analogs, both compound 1 and compound 2 exhibit stronger affinity for monkey NPC1L1 compared to human NPC1L1. The substitution of the methyl ester on the glucuronide in compound 2 confers much higher affinity to both human and monkey NPC1L1. The methyl ester conveys a 20-fold increase in binding to human NPC1L1 and a 3-fold increase at monkey NPC1L1.

The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

Patents, patent applications, publications, product descriptions, and protocols are cited throughout this application, the disclosures of which are incorporated herein by reference in their entireties for all purposes. 

1. An isolated polypeptide comprising an amino acid sequence that is at least 97% identical to the amino acid sequence set forth in SEQ ID NO: 8 wherein said polypeptide binds to the compound having the structural formula

with a K_(i) of 92 nM or lower.
 2. The isolated polypeptide of claim 1 comprising the amino acid sequence set forth in SEQ ID NO:
 8. 3. The polypeptide of claim 1 which is antigenic.
 4. An isolated fusion polypeptide comprising the polypeptide of claim 1 which is radiolabeled or fused to a heterologous polypeptide.
 5. The fusion polypeptide of claim 4 wherein: (a) the heterologous polypeptide is a member selected from the group consisting of: glutathione-S-transferase, a hexahistidine tag, a green fluorescent protein tag, a maltose binding protein tag, a haemagglutinin tag, a cellulose binding protein tag and a myc tag; or (b) the radiolabel is a member selected from the group consisting of ³²P, ³⁵S, ³H, ¹⁴C, ¹²³I, ¹¹¹In, ⁶⁸Ga, ¹⁸F, ¹²⁵I, ¹³¹I, ^(113m)In, ⁷⁶Br, ⁶⁷Ga and ^(99m)Tc.
 6. The polypeptide of claim 1 complexed with a compound selected from the group consisting of structural formula 1, 2, 3, 4, 5, 6, 7, 8, 9, a sterol, and a 5α-stanol.
 7. The polypeptide of claim 6 wherein the sterol is cholesterol.
 8. The polypeptide of claim 6 wherein said compound represented by structural formula 1, 2, 3, 4, 5, 6, 7, 8 or 9, the sterol or the 5α-stanol is detectably labeled.
 9. The polypeptide of claim 8 wherein the label is ³H or ¹²⁵I.
 10. An isolated polypeptide comprising an amino acid sequence that is at least 97% identical to the amino acid sequence set forth in SEQ ID NO: 8 wherein said polypeptide binds to the compound having the structural formula

with a K_(i) of 92 nM or lower; wherein the polypeptide is produced by a method comprising culturing a host cell comprising a polynucleotide encoding said polypeptide, in a vector, under conditions in which the polypeptide is expressed.
 11. A method for identifying an antagonist of NPC1L1 comprising: (a) contacting the polypeptide of claim 1, in the presence of a known amount of a detectable or detectably labeled substance which is known to bind to said polypeptide, with a sample to be tested for the presence of the antagonist; and (b) measuring the amount of the detectable or detectably labeled substance specifically bound to the polypeptide; wherein an NPC1L1 antagonist in the sample is identified by measuring substantially reduced binding of the detectable or detectably labeled substance to the polypeptide, compared to what would be measured in the absence of such an antagonist.
 12. A method for identifying an antagonist of NPC1L1 comprising: (a) placing, in an aqueous suspension, a plurality of support particles, impregnated with a fluorescer, to which the polypeptide of claim 1 is attached; (b) adding, to the suspension, a radiolabeled substance which is known to bind said polypeptide and a sample to be tested for the presence of the antagonist, wherein the radiolabel emits radiation energy capable of activating the fluorescer upon binding of the substance to the polypeptide to produce light energy, whereas radiolabeled substance that does not bind to the polypeptide is, generally, too far removed from the support particles to enable the radioactive energy to activate the fluorescer; and (c) measuring the light energy emitted by the fluorescer in the suspension; wherein an NPC1L1 antagonist in the sample is identified by measuring substantially reduced light energy emission, compared to what would be measured in the absence of such an antagonist.
 13. The method of claim 12 wherein the fluorescer is selected from yttrium silicate, yttrium oxide, diphenyloxazole and polyvinyltoluene.
 14. A method of claim 11 wherein the substance is a radiolabeled sterol, a radiolabeled 5α-stanol or a radiolabeled compound represented by a structural formula selected from 1-9.
 15. A method of claim 12 wherein the substance is a radiolabeled sterol, a radiolabeled 5α-stanol or a radiolabeled compound represented by a structural formula selected from 1-9.
 16. A method for identifying an antagonist of NPC1L1 comprising: (a) contacting a host cell expressing, on its cell surface, the polypeptide of claim 1 with a detectably labeled sterol or 5α-stanol and with a sample to be tested for the presence of the antagonist; and (b) measuring the amount of detectably labeled sterol or 5α-stanol in the cell; wherein an NPC1L1 antagonist in the sample is identified by measuring substantially reduced detectably labeled sterol or 5α-stanol within the host cell, compared to what would be measured in the absence of such an antagonist.
 17. The method of claim 16 wherein the sterol or 5α-stanol is detectably labeled with a radiolabel selected from ³H, ¹⁴C and ¹²⁵I.
 18. The method of claim 16 wherein the sterol is cholesterol.
 19. A method of claim 11 wherein the polypeptide is on a cell membrane of a host cell or in a membrane fraction thereof.
 20. A method according to claim 12 wherein the polypeptide is on a cell membrane of a host cell or in a membrane fraction thereof.
 21. A method according to claim 16 wherein the polypeptide is on a cell membrane of a host cell or in a membrane fraction thereof.
 22. A method for screening a sample for an intestinal sterol or 5α-stanol absorption antagonist comprising: (a) feeding a sterol or 5α-stanol-containing substance to a first and second animal which is a rhesus monkey comprising a functional NPC1L1 gene that encodes the polypeptide of claim 1 and to a third, mutant animal which is a rhesus monkey which does not comprise a functional NPC1L1 gene; (b) administering the sample to be tested for the presence of the antagonist to the first animal, and optionally to the third animal, but not the second animal; (c) measuring the amount of sterol or 5α-stanol absorption in the intestine of said first, second and third animals; and (d) comparing the levels of intestinal sterol or 5α-stanol absorption in said first, second and third animals; wherein the sample is determined to contain the intestinal sterol or 5α-stanol absorption antagonist when the level of intestinal sterol or 5α-stanol absorption in the first animal and the third animal are less than the amount of intestinal sterol or 5α-stanol absorption in the second animal.
 23. The method of claim 22 wherein the sterol is cholesterol.
 24. The method of claim 23 wherein the cholesterol is radiolabeled.
 25. The method of claim 22 wherein the level of sterol or 5α-stanol cholesterol absorption is determined by measuring the level of serum sterol or 5α-stanol in the animal.
 26. A method for identifying an inhibitor of cholesterol absorption comprising the steps of: providing a cell expressing the polypeptide of claim 1 which cell is capable of binding a fluorescent cholesterol absorption inhibitor; contacting said cell with a candidate inhibitor of cholesterol absorption in the presence of said fluorescent cholesterol absorption inhibitor; and measuring fluorescence of said cell, wherein a relative absence of fluorescent cholesterol absorption inhibitor indicates that said candidate inhibitory agent is an inhibitor of cholesterol absorption which inhibits cholesterol absorption.
 27. The method of claim 26 wherein the inhibitor is an azetidinone.
 28. The method of claim 26 wherein the fluorescent cholesterol absorption inhibitor is

wherein R comprises a fluorescent moiety.
 29. The method of claim 28, wherein R is a fluorescent moiety linked by an alkynyl-containing tether group.
 30. The method of claim 29, wherein R is selected from the group consisting of:


31. A method for identifying an inhibitor of intestinal absorption of cholesterol, said method comprising the steps of: (a) combining a fluorescent cholesterol absorption inhibitor, a cell membrane comprising the polypeptide of claim 1, and a candidate inhibitor of intestinal cholesterol absorption, under conditions wherein, but for the presence of said inhibitor, said fluorescent cholesterol absorption inhibitor is bound to the NPC1L1 in the membrane; and (b) detecting the relative presence or absence of fluorescent cholesterol absorption inhibitor bound to the membrane, wherein a relative absence of fluorescent cholesterol absorption inhibitor indicates that said candidate inhibitor of intestinal cholesterol absorption is an inhibitor of intestinal cholesterol absorption which inhibits intestinal cholesterol absorption.
 32. The method of claim 31 wherein the inhibitor is an azetidinone.
 33. The method of claim 31 wherein the fluorescent cholesterol absorption inhibitor is

wherein R comprises a fluorescent moiety.
 34. The method of claim 33, wherein R is a fluorescent moiety linked by an alkynyl-containing tether group.
 35. The method of claim 34, wherein R is selected from the group consisting of: 